Example 1: Preprocessing Workflow¶
This is meant as a very simple example for a preprocessing workflow. In this workflow we will conduct the following steps:
- Motion correction of functional images with FSL's MCFLIRT
- Coregistration of functional images to anatomical images (according to FSL's FEAT pipeline)
- Smoothing of coregistered functional images with FWHM set to 4mm and 8mm
- Artifact Detection in functional images (to detect outlier volumes)
Preparation¶
Before we can start with anything we first need to download the data (the other 9 subjects in the dataset). This can be done very quickly with the following datalad command.
Note: This might take a while, as datalad needs to download ~700MB of data
In [ ]:
%%bash
datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \
/data/ds000114/sub-*/ses-test/func/*fingerfootlips*
get(notneeded): /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz (file) [already present] get(notneeded): /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_space-mni152nlin2009casym_preproc.nii.gz (file) [already present] action summary: get (notneeded: 30)
Inspect the data¶
For every subject we have one anatomical T1w and 5 functional images. As a short recap, the image properties of the anatomy and the fingerfootlips functional image are:
In [ ]:
%%bash
cd /data/ds000114/
nib-ls derivatives/fmriprep/sub-01/*/*t1w_preproc.nii.gz sub-01/ses-test/f*/*fingerfootlips*.nii.gz
derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz float32 [256, 156, 256] 1.00x1.30x1.00 sform sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz int16 [ 64, 64, 30, 184] 4.00x4.00x4.00x2.50 sform
So, let's start!
Imports¶
First, let's import all the modules we later will be needing.
In [ ]:
%matplotlib inline
from os.path import join as opj
import os
import json
from nipype.interfaces.fsl import (BET, ExtractROI, FAST, FLIRT, ImageMaths,
MCFLIRT, SliceTimer, Threshold)
from nipype.interfaces.spm import Smooth
from nipype.interfaces.utility import IdentityInterface
from nipype.interfaces.io import SelectFiles, DataSink
from nipype.algorithms.rapidart import ArtifactDetect
from nipype import Workflow, Node
Experiment parameters¶
It's always a good idea to specify all parameters that might change between experiments at the beginning of your script. We will use one functional image for fingerfootlips task for ten subjects.
In [ ]:
experiment_dir = '/output'
output_dir = 'datasink'
working_dir = 'workingdir'
# list of subject identifiers
subject_list = ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']
# list of session identifiers
task_list = ['fingerfootlips']
# Smoothing widths to apply
fwhm = [4, 8]
# TR of functional images
with open('/data/ds000114/task-fingerfootlips_bold.json', 'rt') as fp:
task_info = json.load(fp)
TR = task_info['RepetitionTime']
# Isometric resample of functional images to voxel size (in mm)
iso_size = 4
Specify Nodes for the main workflow¶
Initiate all the different interfaces (represented as nodes) that you want to use in your workflow.
In [ ]:
# ExtractROI - skip dummy scans
extract = Node(ExtractROI(t_min=4, t_size=-1, output_type='NIFTI'),
name="extract")
# MCFLIRT - motion correction
mcflirt = Node(MCFLIRT(mean_vol=True,
save_plots=True,
output_type='NIFTI'),
name="mcflirt")
# SliceTimer - correct for slice wise acquisition
slicetimer = Node(SliceTimer(index_dir=False,
interleaved=True,
output_type='NIFTI',
time_repetition=TR),
name="slicetimer")
# Smooth - image smoothing
smooth = Node(Smooth(), name="smooth")
smooth.iterables = ("fwhm", fwhm)
# Artifact Detection - determines outliers in functional images
art = Node(ArtifactDetect(norm_threshold=2,
zintensity_threshold=3,
mask_type='spm_global',
parameter_source='FSL',
use_differences=[True, False],
plot_type='svg'),
name="art")
Coregistration Workflow¶
Initiate a workflow that coregistrates the functional images to the anatomical image (according to FSL's FEAT pipeline).
In [ ]:
# BET - Skullstrip anatomical Image
bet_anat = Node(BET(frac=0.5,
robust=True,
output_type='NIFTI_GZ'),
name="bet_anat")
# FAST - Image Segmentation
segmentation = Node(FAST(output_type='NIFTI_GZ'),
name="segmentation")
# Select WM segmentation file from segmentation output
def get_wm(files):
return files[-1]
# Threshold - Threshold WM probability image
threshold = Node(Threshold(thresh=0.5,
args='-bin',
output_type='NIFTI_GZ'),
name="threshold")
# FLIRT - pre-alignment of functional images to anatomical images
coreg_pre = Node(FLIRT(dof=6, output_type='NIFTI_GZ'),
name="coreg_pre")
# FLIRT - coregistration of functional images to anatomical images with BBR
coreg_bbr = Node(FLIRT(dof=6,
cost='bbr',
schedule=opj(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch'),
output_type='NIFTI_GZ'),
name="coreg_bbr")
# Apply coregistration warp to functional images
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI'),
name="applywarp")
# Apply coregistration warp to mean file
applywarp_mean = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI_GZ'),
name="applywarp_mean")
# Create a coregistration workflow
coregwf = Workflow(name='coregwf')
coregwf.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the coregistration workflow
coregwf.connect([(bet_anat, segmentation, [('out_file', 'in_files')]),
(segmentation, threshold, [(('partial_volume_files', get_wm),
'in_file')]),
(bet_anat, coreg_pre, [('out_file', 'reference')]),
(threshold, coreg_bbr, [('out_file', 'wm_seg')]),
(coreg_pre, coreg_bbr, [('out_matrix_file', 'in_matrix_file')]),
(coreg_bbr, applywarp, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp, [('out_file', 'reference')]),
(coreg_bbr, applywarp_mean, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp_mean, [('out_file', 'reference')]),
])
Specify input & output stream¶
Specify where the input data can be found & where and how to save the output data.
In [ ]:
# Infosource - a function free node to iterate over the list of subject names
infosource = Node(IdentityInterface(fields=['subject_id', 'task_name']),
name="infosource")
infosource.iterables = [('subject_id', subject_list),
('task_name', task_list)]
# SelectFiles - to grab the data (alternativ to DataGrabber)
anat_file = opj('derivatives', 'fmriprep', 'sub-{subject_id}', 'anat', 'sub-{subject_id}_t1w_preproc.nii.gz')
func_file = opj('sub-{subject_id}', 'ses-test', 'func',
'sub-{subject_id}_ses-test_task-{task_name}_bold.nii.gz')
templates = {'anat': anat_file,
'func': func_file}
selectfiles = Node(SelectFiles(templates,
base_directory='/data/ds000114'),
name="selectfiles")
# Datasink - creates output folder for important outputs
datasink = Node(DataSink(base_directory=experiment_dir,
container=output_dir),
name="datasink")
## Use the following DataSink output substitutions
substitutions = [('_subject_id_', 'sub-'),
('_task_name_', '/task-'),
('_fwhm_', 'fwhm-'),
('_roi', ''),
('_mcf', ''),
('_st', ''),
('_flirt', ''),
('.nii_mean_reg', '_mean'),
('.nii.par', '.par'),
]
subjFolders = [('fwhm-%s/' % f, 'fwhm-%s_' % f) for f in fwhm]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
Specify Workflow¶
Create a workflow and connect the interface nodes and the I/O stream to each other.
In [ ]:
# Create a preprocessing workflow
preproc = Workflow(name='preproc')
preproc.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the preprocessing workflow
preproc.connect([(infosource, selectfiles, [('subject_id', 'subject_id'),
('task_name', 'task_name')]),
(selectfiles, extract, [('func', 'in_file')]),
(extract, mcflirt, [('roi_file', 'in_file')]),
(mcflirt, slicetimer, [('out_file', 'in_file')]),
(selectfiles, coregwf, [('anat', 'bet_anat.in_file'),
('anat', 'coreg_bbr.reference')]),
(mcflirt, coregwf, [('mean_img', 'coreg_pre.in_file'),
('mean_img', 'coreg_bbr.in_file'),
('mean_img', 'applywarp_mean.in_file')]),
(slicetimer, coregwf, [('slice_time_corrected_file', 'applywarp.in_file')]),
(coregwf, smooth, [('applywarp.out_file', 'in_files')]),
(mcflirt, datasink, [('par_file', 'preproc.@par')]),
(smooth, datasink, [('smoothed_files', 'preproc.@smooth')]),
(coregwf, datasink, [('applywarp_mean.out_file', 'preproc.@mean')]),
(coregwf, art, [('applywarp.out_file', 'realigned_files')]),
(mcflirt, art, [('par_file', 'realignment_parameters')]),
(coregwf, datasink, [('coreg_bbr.out_matrix_file', 'preproc.@mat_file'),
('bet_anat.out_file', 'preproc.@brain')]),
(art, datasink, [('outlier_files', 'preproc.@outlier_files'),
('plot_files', 'preproc.@plot_files')]),
])
Visualize the workflow¶
It always helps to visualize your workflow.
In [ ]:
# Create preproc output graph
preproc.write_graph(graph2use='colored', format='png', simple_form=True)
# Visualize the graph
from IPython.display import Image
Image(filename=opj(preproc.base_dir, 'preproc', 'graph.png'))
180514-09:58:05,87 workflow INFO: Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=colored, simple_form=True).
Out[ ]:
In [ ]:
# Visualize the detailed graph
preproc.write_graph(graph2use='flat', format='png', simple_form=True)
Image(filename=opj(preproc.base_dir, 'preproc', 'graph_detailed.png'))
180514-09:58:05,755 workflow INFO: Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=flat, simple_form=True).
Out[ ]:
Run the Workflow¶
Now that everything is ready, we can run the preprocessing workflow. Change n_procs to the number of jobs/cores you want to use. Note that if you're using a Docker container and FLIRT fails to run without any good reason, you might need to change memory settings in the Docker preferences (6 GB should be enough for this workflow).
In [ ]:
preproc.run('MultiProc', plugin_args={'n_procs': 8})
180514-10:24:39,491 workflow INFO:
Workflow preproc settings: ['check', 'execution', 'logging', 'monitoring']
180514-10:24:39,630 workflow INFO:
Running in parallel.
180514-10:24:39,640 workflow INFO:
[MultiProc] Running 0 tasks, and 10 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:24:39,704 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles".180514-10:24:39,705 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles".
180514-10:24:39,715 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:24:39,712 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:24:39,715 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles".
180514-10:24:39,719 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles".
180514-10:24:39,725 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:24:39,726 workflow INFO:
[Node] Finished "preproc.selectfiles".180514-10:24:39,728 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:39,713 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles".180514-10:24:39,710 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles".180514-10:24:39,728 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:24:39,707 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles".180514-10:24:39,736 workflow INFO:
[Node] Finished "preproc.selectfiles".180514-10:24:39,741 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:24:39,741 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:24:39,745 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:39,751 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:24:39,713 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles".
180514-10:24:39,755 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:39,761 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:24:39,763 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:39,771 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:39,780 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:24:41,640 workflow INFO:
[Job 0] Completed (preproc.selectfiles).
180514-10:24:41,642 workflow INFO:
[Job 16] Completed (preproc.selectfiles).
180514-10:24:41,645 workflow INFO:
[Job 32] Completed (preproc.selectfiles).
180514-10:24:41,647 workflow INFO:
[Job 48] Completed (preproc.selectfiles).
180514-10:24:41,650 workflow INFO:
[Job 64] Completed (preproc.selectfiles).
180514-10:24:41,652 workflow INFO:
[Job 80] Completed (preproc.selectfiles).
180514-10:24:41,654 workflow INFO:
[Job 96] Completed (preproc.selectfiles).
180514-10:24:41,656 workflow INFO:
[Job 112] Completed (preproc.selectfiles).
180514-10:24:41,659 workflow INFO:
[MultiProc] Running 0 tasks, and 18 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:24:41,706 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat".
180514-10:24:41,709 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract".
180514-10:24:41,712 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -f 0.50 -R180514-10:24:41,712 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat".
180514-10:24:41,719 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract".
180514-10:24:41,720 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:24:41,724 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat".180514-10:24:41,726 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -f 0.50 -R180514-10:24:41,727 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract".
180514-10:24:41,733 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii 4 -1180514-10:24:41,733 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat".
180514-10:24:41,734 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:24:41,740 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract".
180514-10:24:41,746 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -f 0.50 -R180514-10:24:41,748 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:24:41,761 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:24:42,660 workflow INFO:
[Node] Finished "preproc.extract".180514-10:24:42,666 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:24:42,804 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:24:42,846 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:24:43,646 workflow INFO:
[Job 4] Completed (preproc.extract).
180514-10:24:43,649 workflow INFO:
[Job 20] Completed (preproc.extract).
180514-10:24:43,653 workflow INFO:
[Job 36] Completed (preproc.extract).
180514-10:24:43,657 workflow INFO:
[Job 52] Completed (preproc.extract).
180514-10:24:43,663 workflow INFO:
[MultiProc] Running 4 tasks, and 14 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
180514-10:24:43,729 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt".180514-10:24:43,734 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt".180514-10:24:43,741 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt".180514-10:24:43,736 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt".
180514-10:24:43,762 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots180514-10:24:43,763 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:24:43,768 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots180514-10:24:43,774 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:24:45,651 workflow INFO:
[MultiProc] Running 8 tasks, and 10 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
180514-10:24:54,874 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:24:55,656 workflow INFO:
[Job 49] Completed (preproc.coregwf.bet_anat).
180514-10:24:55,687 workflow INFO:
[MultiProc] Running 7 tasks, and 11 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
180514-10:24:55,772 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation".
180514-10:24:55,805 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain.nii.gz
180514-10:24:57,661 workflow INFO:
[MultiProc] Running 8 tasks, and 10 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
180514-10:25:03,862 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:25:04,639 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:25:05,89 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:25:05,666 workflow INFO:
[Job 1] Completed (preproc.coregwf.bet_anat).
180514-10:25:05,668 workflow INFO:
[Job 17] Completed (preproc.coregwf.bet_anat).
180514-10:25:05,672 workflow INFO:
[Job 33] Completed (preproc.coregwf.bet_anat).
180514-10:25:05,676 workflow INFO:
[MultiProc] Running 5 tasks, and 13 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
180514-10:25:05,736 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation".180514-10:25:05,739 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation".
180514-10:25:05,747 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation".
180514-10:25:05,756 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain.nii.gz180514-10:25:05,763 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain.nii.gz
180514-10:25:05,783 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain.nii.gz
180514-10:25:07,668 workflow INFO:
[MultiProc] Running 8 tasks, and 10 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
180514-10:26:43,469 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:26:43,762 workflow INFO:
[Job 53] Completed (preproc.mcflirt).
180514-10:26:43,780 workflow INFO:
[MultiProc] Running 7 tasks, and 12 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
180514-10:26:43,897 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre".
180514-10:26:43,911 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:26:45,768 workflow INFO:
[MultiProc] Running 8 tasks, and 11 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
180514-10:26:46,443 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:26:47,768 workflow INFO:
[Job 5] Completed (preproc.mcflirt).
180514-10:26:47,775 workflow INFO:
[MultiProc] Running 7 tasks, and 13 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
180514-10:26:47,903 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre".
180514-10:26:47,933 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:26:49,774 workflow INFO:
[MultiProc] Running 8 tasks, and 12 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
180514-10:26:52,387 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:26:53,167 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:26:53,776 workflow INFO:
[Job 21] Completed (preproc.mcflirt).
180514-10:26:53,778 workflow INFO:
[Job 37] Completed (preproc.mcflirt).
180514-10:26:53,783 workflow INFO:
[MultiProc] Running 6 tasks, and 16 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:26:53,875 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer".180514-10:26:53,878 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre".
180514-10:26:53,886 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000180514-10:26:53,908 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:26:55,780 workflow INFO:
[MultiProc] Running 8 tasks, and 14 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:26:56,766 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:26:57,780 workflow INFO:
[Job 54] Completed (preproc.coregwf.coreg_pre).
180514-10:26:57,805 workflow INFO:
[MultiProc] Running 7 tasks, and 14 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:26:57,869 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer".
180514-10:26:57,901 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:26:59,786 workflow INFO:
[MultiProc] Running 8 tasks, and 13 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:00,630 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:27:01,787 workflow INFO:
[Job 9] Completed (preproc.slicetimer).
180514-10:27:01,798 workflow INFO:
[MultiProc] Running 7 tasks, and 13 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:01,867 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre".
180514-10:27:01,910 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:27:03,351 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:27:03,790 workflow INFO:
[Job 6] Completed (preproc.coregwf.coreg_pre).
180514-10:27:03,816 workflow INFO:
[MultiProc] Running 7 tasks, and 12 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:03,966 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer".
180514-10:27:04,605 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:27:05,373 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:27:05,794 workflow INFO:
[Job 25] Completed (preproc.slicetimer).
180514-10:27:05,814 workflow INFO:
[MultiProc] Running 7 tasks, and 11 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:05,902 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer".
180514-10:27:05,923 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:27:07,797 workflow INFO:
[MultiProc] Running 8 tasks, and 10 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:10,182 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:27:11,798 workflow INFO:
[Job 22] Completed (preproc.coregwf.coreg_pre).
180514-10:27:11,823 workflow INFO:
[MultiProc] Running 7 tasks, and 10 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:11,913 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat".
180514-10:27:11,940 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:27:12,283 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:27:13,100 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:27:13,802 workflow INFO:
[Job 41] Completed (preproc.slicetimer).
180514-10:27:13,803 workflow INFO:
[Job 57] Completed (preproc.slicetimer).
180514-10:27:13,810 workflow INFO:
[MultiProc] Running 6 tasks, and 9 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:13,863 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract".180514-10:27:13,865 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat".
180514-10:27:13,901 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -f 0.50 -R180514-10:27:13,892 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:27:14,760 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:27:15,806 workflow INFO:
[Job 68] Completed (preproc.extract).
180514-10:27:15,814 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:15,885 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt".
180514-10:27:15,913 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:27:17,811 workflow INFO:
[MultiProc] Running 8 tasks, and 7 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:18,420 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:27:19,812 workflow INFO:
[Job 38] Completed (preproc.coregwf.coreg_pre).
180514-10:27:19,819 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:19,882 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract".
180514-10:27:19,936 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:27:21,261 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:27:21,816 workflow INFO:
[Job 84] Completed (preproc.extract).
180514-10:27:21,831 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:21,929 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt".
180514-10:27:21,945 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:27:23,822 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:29,425 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:27:29,830 workflow INFO:
[Job 81] Completed (preproc.coregwf.bet_anat).
180514-10:27:29,839 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:29,903 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation".
180514-10:27:29,921 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain.nii.gz
180514-10:27:30,25 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:27:31,834 workflow INFO:
[Job 65] Completed (preproc.coregwf.bet_anat).
180514-10:27:31,877 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:27:31,995 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation".
180514-10:27:32,18 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain.nii.gz
180514-10:27:33,840 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:26,871 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:29:27,956 workflow INFO:
[Job 85] Completed (preproc.mcflirt).
180514-10:29:27,964 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:28,64 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre".
180514-10:29:28,106 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:29:28,686 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:29:29,961 workflow INFO:
[Job 69] Completed (preproc.mcflirt).
180514-10:29:29,969 workflow INFO:
[MultiProc] Running 7 tasks, and 9 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:30,64 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre".
180514-10:29:30,97 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:29:31,966 workflow INFO:
[MultiProc] Running 8 tasks, and 8 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:43,797 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:29:43,976 workflow INFO:
[Job 86] Completed (preproc.coregwf.coreg_pre).
180514-10:29:44,2 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:44,73 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer".
180514-10:29:44,114 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:29:45,980 workflow INFO:
[MultiProc] Running 8 tasks, and 7 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:46,296 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:29:47,980 workflow INFO:
[Job 70] Completed (preproc.coregwf.coreg_pre).
180514-10:29:47,986 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:48,61 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer".
180514-10:29:48,80 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:29:49,984 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.slicetimer
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:51,106 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:29:51,984 workflow INFO:
[Job 73] Completed (preproc.slicetimer).
180514-10:29:51,990 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:52,94 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat".
180514-10:29:52,139 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:29:53,988 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.slicetimer
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:56,380 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:29:57,990 workflow INFO:
[Job 89] Completed (preproc.slicetimer).
180514-10:29:58,0 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:29:58,72 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract".
180514-10:29:58,112 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:29:58,930 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:29:59,997 workflow INFO:
[Job 100] Completed (preproc.extract).
180514-10:30:00,6 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:00,111 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt".
180514-10:30:00,137 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:30:02,1 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:09,144 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:30:10,9 workflow INFO:
[Job 2] Completed (preproc.coregwf.segmentation).
180514-10:30:10,23 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:10,106 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold".
180514-10:30:10,147 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:11,390 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:30:11,468 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:30:12,13 workflow INFO:
[Job 97] Completed (preproc.coregwf.bet_anat).
180514-10:30:12,19 workflow INFO:
[Job 3] Completed (preproc.coregwf.threshold).
180514-10:30:12,27 workflow INFO:
[MultiProc] Running 6 tasks, and 6 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:12,124 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr".180514-10:30:12,126 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation".
180514-10:30:12,164 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain.nii.gz180514-10:30:12,175 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:14,16 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:15,693 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:30:16,19 workflow INFO:
[Job 18] Completed (preproc.coregwf.segmentation).
180514-10:30:16,32 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:16,27 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:30:16,102 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold".
180514-10:30:16,126 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:17,103 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:30:18,21 workflow INFO:
[Job 50] Completed (preproc.coregwf.segmentation).
180514-10:30:18,24 workflow INFO:
[Job 19] Completed (preproc.coregwf.threshold).
180514-10:30:18,28 workflow INFO:
[MultiProc] Running 6 tasks, and 6 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:18,95 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr".
180514-10:30:18,106 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz180514-10:30:18,103 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold".
180514-10:30:18,140 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:19,370 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:30:20,21 workflow INFO:
[Job 51] Completed (preproc.coregwf.threshold).
180514-10:30:20,46 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:20,143 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr".
180514-10:30:20,181 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:22,26 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:42,465 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:30:44,50 workflow INFO:
[Job 34] Completed (preproc.coregwf.segmentation).
180514-10:30:44,84 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:44,166 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold".
180514-10:30:44,195 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:45,575 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:30:46,54 workflow INFO:
[Job 35] Completed (preproc.coregwf.threshold).
180514-10:30:46,88 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:30:46,234 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr".
180514-10:30:46,264 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:30:48,61 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:00,183 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:32:02,170 workflow INFO:
[Job 101] Completed (preproc.mcflirt).
180514-10:32:02,190 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:02,281 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre".
180514-10:32:02,326 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:32:04,176 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:19,699 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:32:20,190 workflow INFO:
[Job 102] Completed (preproc.coregwf.coreg_pre).
180514-10:32:20,195 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:20,248 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer".
180514-10:32:20,291 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:32:22,196 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:28,422 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:32:30,200 workflow INFO:
[Job 105] Completed (preproc.slicetimer).
180514-10:32:30,220 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:30,282 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat".
180514-10:32:30,322 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:32:32,205 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:32:47,9 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:32:48,218 workflow INFO:
[Job 66] Completed (preproc.coregwf.segmentation).
180514-10:32:48,225 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:32:48,278 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold".
180514-10:32:48,319 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:32:49,634 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:32:50,222 workflow INFO:
[Job 67] Completed (preproc.coregwf.threshold).
180514-10:32:50,226 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:32:50,325 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr".
180514-10:32:50,358 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:32:52,228 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:32:56,589 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:32:58,232 workflow INFO:
[Job 113] Completed (preproc.coregwf.bet_anat).
180514-10:32:58,238 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:32:58,310 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation".
180514-10:32:58,340 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain.nii.gz
180514-10:33:00,238 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:33:14,974 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:33:16,266 workflow INFO:
[Job 82] Completed (preproc.coregwf.segmentation).
180514-10:33:16,273 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:33:16,342 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold".
180514-10:33:16,394 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:33:17,701 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:33:18,270 workflow INFO:
[Job 83] Completed (preproc.coregwf.threshold).
180514-10:33:18,307 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:33:18,390 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr".
180514-10:33:18,431 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:33:20,276 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:34:03,81 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:34:03,445 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:34:04,318 workflow INFO:
[Job 7] Completed (preproc.coregwf.coreg_bbr).
180514-10:34:04,320 workflow INFO:
[Job 55] Completed (preproc.coregwf.coreg_bbr).
180514-10:34:04,325 workflow INFO:
[MultiProc] Running 6 tasks, and 7 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:04,375 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp_mean".
180514-10:34:04,381 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp".180514-10:34:04,391 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:04,403 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:06,324 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:07,474 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:34:08,324 workflow INFO:
[Job 8] Completed (preproc.coregwf.applywarp_mean).
180514-10:34:08,347 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:08,421 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp_mean".
180514-10:34:08,465 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:10,330 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:11,607 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:34:12,330 workflow INFO:
[Job 56] Completed (preproc.coregwf.applywarp_mean).
180514-10:34:12,359 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:12,423 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp".
180514-10:34:12,453 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:14,336 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:22,151 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:34:22,342 workflow INFO:
[Job 23] Completed (preproc.coregwf.coreg_bbr).
180514-10:34:22,356 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:22,434 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp_mean".
180514-10:34:22,462 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:23,71 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:34:24,346 workflow INFO:
[Job 10] Completed (preproc.coregwf.applywarp).
180514-10:34:24,374 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:24,440 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:34:24,469 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:34:25,634 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:34:26,350 workflow INFO:
[Job 24] Completed (preproc.coregwf.applywarp_mean).
180514-10:34:26,368 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:26,436 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:34:26,458 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:34:28,356 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:31,120 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:34:32,358 workflow INFO:
[Job 58] Completed (preproc.coregwf.applywarp).
180514-10:34:32,362 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:32,423 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/art".
180514-10:34:32,441 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:34:33,116 workflow INFO:
[Node] Finished "preproc.art".
180514-10:34:34,362 workflow INFO:
[Job 13] Completed (preproc.art).
180514-10:34:34,380 workflow INFO:
[MultiProc] Running 7 tasks, and 7 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:34,455 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp".
180514-10:34:34,493 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:36,368 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:52,309 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:34:52,382 workflow INFO:
[Job 39] Completed (preproc.coregwf.coreg_bbr).
180514-10:34:52,386 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:52,449 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp_mean".
180514-10:34:52,487 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:34:53,576 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:34:54,386 workflow INFO:
[Job 26] Completed (preproc.coregwf.applywarp).
180514-10:34:54,390 workflow INFO:
[MultiProc] Running 7 tasks, and 10 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:54,482 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:34:54,511 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:34:55,220 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:34:56,390 workflow INFO:
[Job 40] Completed (preproc.coregwf.applywarp_mean).
180514-10:34:56,408 workflow INFO:
[MultiProc] Running 7 tasks, and 9 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:34:56,471 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:34:56,507 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:34:58,396 workflow INFO:
[MultiProc] Running 8 tasks, and 8 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:14,554 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:35:15,896 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:35:16,412 workflow INFO:
[Job 11] Completed (preproc.smooth).
180514-10:35:16,415 workflow INFO:
[Job 12] Completed (preproc.smooth).
180514-10:35:16,443 workflow INFO:
[MultiProc] Running 6 tasks, and 10 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:16,518 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:35:16,532 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-10:35:16,543 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:35:16,563 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz180514-10:35:16,575 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:35:16,603 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt180514-10:35:16,608 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-4_ssub-10_ses-test_task-fingerfootlips_bold.nii
180514-10:35:16,631 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
180514-10:35:16,638 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz180514-10:35:16,657 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:35:16,674 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:35:16,694 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par180514-10:35:16,698 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
180514-10:35:16,716 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-8_ssub-10_ses-test_task-fingerfootlips_bold.nii
180514-10:35:16,713 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:35:16,732 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:35:16,739 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par
180514-10:35:16,758 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:35:16,765 interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:35:16,782 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:35:18,418 workflow INFO:
[Job 14] Completed (preproc.datasink).
180514-10:35:18,420 workflow INFO:
[Job 15] Completed (preproc.datasink).
180514-10:35:18,425 workflow INFO:
[MultiProc] Running 6 tasks, and 8 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:18,491 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp".180514-10:35:18,486 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/art".
180514-10:35:18,516 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:35:18,552 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:35:19,457 workflow INFO:
[Node] Finished "preproc.art".
180514-10:35:20,423 workflow INFO:
[Job 29] Completed (preproc.art).
180514-10:35:20,432 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:20,528 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:35:20,590 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:35:22,428 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:36,15 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:35:36,440 workflow INFO:
[Job 98] Completed (preproc.coregwf.segmentation).
180514-10:35:36,449 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:36,505 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:35:36,557 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:35:37,149 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:35:38,443 workflow INFO:
[Job 42] Completed (preproc.coregwf.applywarp).
180514-10:35:38,451 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:38,547 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:35:38,566 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:35:40,451 workflow INFO:
[MultiProc] Running 8 tasks, and 7 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:46,265 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:35:46,454 workflow INFO:
[Job 27] Completed (preproc.smooth).
180514-10:35:46,459 workflow INFO:
[MultiProc] Running 7 tasks, and 8 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:46,542 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:35:46,581 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:35:46,611 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
180514-10:35:46,629 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:35:46,661 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
180514-10:35:46,679 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:35:46,691 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
180514-10:35:46,717 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-8_ssub-09_ses-test_task-fingerfootlips_bold.nii
180514-10:35:46,746 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:35:46,790 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:35:47,489 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:35:48,458 workflow INFO:
[Job 28] Completed (preproc.smooth).
180514-10:35:48,460 workflow INFO:
[Job 30] Completed (preproc.datasink).
180514-10:35:48,465 workflow INFO:
[MultiProc] Running 6 tasks, and 8 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:48,533 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/datasink".180514-10:35:48,538 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:35:48,563 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")180514-10:35:48,575 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:35:48,594 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-4_ssub-09_ses-test_task-fingerfootlips_bold.nii
180514-10:35:48,628 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
180514-10:35:48,655 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:35:48,698 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
180514-10:35:48,716 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:35:48,739 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
180514-10:35:48,769 interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:35:48,791 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:35:50,463 workflow INFO:
[Job 31] Completed (preproc.datasink).
180514-10:35:50,465 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".180514-10:35:50,468 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:35:50,537 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/art".
180514-10:35:50,571 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
180514-10:35:51,229 workflow INFO:
[Node] Finished "preproc.art".
180514-10:35:52,468 workflow INFO:
[Job 71] Completed (preproc.coregwf.coreg_bbr).
180514-10:35:52,491 workflow INFO:
[Job 45] Completed (preproc.art).
180514-10:35:52,501 workflow INFO:
[MultiProc] Running 6 tasks, and 7 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:52,595 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/art".180514-10:35:52,602 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp_mean".
180514-10:35:52,634 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:35:52,670 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:35:53,691 workflow INFO:
[Node] Finished "preproc.art".
180514-10:35:54,472 workflow INFO:
[Job 61] Completed (preproc.art).
180514-10:35:54,481 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:54,543 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp".
180514-10:35:54,591 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:35:56,143 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:35:56,477 workflow INFO:
[Job 72] Completed (preproc.coregwf.applywarp_mean).
180514-10:35:56,497 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:56,666 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold".
180514-10:35:56,701 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:35:58,166 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:35:58,495 workflow INFO:
[Job 99] Completed (preproc.coregwf.threshold).
180514-10:35:58,522 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:35:58,646 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr".
180514-10:35:58,683 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:36:00,500 workflow INFO:
[MultiProc] Running 8 tasks, and 3 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.applywarp
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:15,839 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:36:16,515 workflow INFO:
[Job 74] Completed (preproc.coregwf.applywarp).
180514-10:36:16,521 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:16,598 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:36:16,618 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:36:18,517 workflow INFO:
[MultiProc] Running 8 tasks, and 5 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:18,712 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:36:20,515 workflow INFO:
[Job 59] Completed (preproc.smooth).
180514-10:36:20,547 workflow INFO:
[MultiProc] Running 7 tasks, and 6 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:20,656 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:36:20,709 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:36:20,726 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
180514-10:36:20,761 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:36:20,786 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
180514-10:36:20,826 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:36:20,854 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
180514-10:36:20,871 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-8_ssub-07_ses-test_task-fingerfootlips_bold.nii
180514-10:36:20,902 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:36:20,936 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:36:22,518 workflow INFO:
[Job 62] Completed (preproc.datasink).
180514-10:36:22,523 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:22,593 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:36:22,602 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:36:24,522 workflow INFO:
[MultiProc] Running 8 tasks, and 4 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:29,307 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:36:30,528 workflow INFO:
[Job 43] Completed (preproc.smooth).
180514-10:36:30,552 workflow INFO:
[MultiProc] Running 7 tasks, and 5 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:30,655 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:36:30,705 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:36:30,751 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
180514-10:36:30,786 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:36:30,822 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
180514-10:36:30,863 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:36:30,897 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
180514-10:36:30,921 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-8_ssub-08_ses-test_task-fingerfootlips_bold.nii
180514-10:36:30,946 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:36:30,968 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:36:32,535 workflow INFO:
[Job 46] Completed (preproc.datasink).
180514-10:36:32,577 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:32,726 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/art".
180514-10:36:32,762 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:36:33,562 workflow INFO:
[Node] Finished "preproc.art".
180514-10:36:34,541 workflow INFO:
[Job 77] Completed (preproc.art).
180514-10:36:34,565 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:34,621 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:36:34,649 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract".
180514-10:36:34,671 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:36:35,530 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:36:36,545 workflow INFO:
[Job 60] Completed (preproc.smooth).
180514-10:36:36,547 workflow INFO:
[Job 116] Completed (preproc.extract).
180514-10:36:36,552 workflow INFO:
[MultiProc] Running 6 tasks, and 4 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:36,616 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/datasink".180514-10:36:36,617 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt".
180514-10:36:36,630 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:36:36,649 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:36:36,666 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-4_ssub-07_ses-test_task-fingerfootlips_bold.nii
180514-10:36:36,686 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
180514-10:36:36,692 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:36:36,697 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
180514-10:36:36,706 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:36:36,715 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
180514-10:36:36,729 interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:36:36,747 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:36:37,546 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:36:38,546 workflow INFO:
[Job 44] Completed (preproc.smooth).
180514-10:36:38,579 workflow INFO:
[Job 63] Completed (preproc.datasink).
180514-10:36:38,596 workflow INFO:
[MultiProc] Running 6 tasks, and 3 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:38,664 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles".180514-10:36:38,661 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:36:38,686 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:36:38,727 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-4_ssub-08_ses-test_task-fingerfootlips_bold.nii
180514-10:36:38,757 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
180514-10:36:38,781 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:36:38,805 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:36:38,813 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
180514-10:36:38,846 workflow INFO:
[Node] Finished "preproc.selectfiles".180514-10:36:38,849 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:36:38,878 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
180514-10:36:38,894 interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:36:38,930 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:36:40,554 workflow INFO:
[Job 47] Completed (preproc.datasink).
180514-10:36:40,562 workflow INFO:
[Job 128] Completed (preproc.selectfiles).
180514-10:36:40,575 workflow INFO:
[MultiProc] Running 6 tasks, and 3 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:40,641 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat".
180514-10:36:40,645 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract".
180514-10:36:40,663 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:36:40,686 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:36:41,673 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:36:42,558 workflow INFO:
[Job 132] Completed (preproc.extract).
180514-10:36:42,564 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:42,616 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt".
180514-10:36:42,644 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:36:44,564 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:48,552 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:36:50,567 workflow INFO:
[Job 87] Completed (preproc.coregwf.coreg_bbr).
180514-10:36:50,578 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:50,726 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp_mean".
180514-10:36:50,759 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:36:52,574 workflow INFO:
[MultiProc] Running 8 tasks, and 2 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:54,162 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:36:54,575 workflow INFO:
[Job 88] Completed (preproc.coregwf.applywarp_mean).
180514-10:36:54,583 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:36:54,668 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp".
180514-10:36:54,703 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:36:56,580 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:05,989 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:37:06,585 workflow INFO:
[Job 129] Completed (preproc.coregwf.bet_anat).
180514-10:37:06,590 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:06,664 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation".
180514-10:37:06,678 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain.nii.gz
180514-10:37:08,591 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.mcflirt
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:08,742 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:37:10,590 workflow INFO:
[Job 76] Completed (preproc.smooth).
180514-10:37:10,594 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.mcflirt
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:10,659 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:37:10,691 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:37:10,700 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-4_ssub-06_ses-test_task-fingerfootlips_bold.nii
180514-10:37:10,705 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
180514-10:37:10,719 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:37:10,745 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg
180514-10:37:10,760 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:37:10,774 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
180514-10:37:10,784 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:37:10,799 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:37:11,941 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:37:11,941 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:37:12,595 workflow INFO:
[Job 75] Completed (preproc.smooth).
180514-10:37:12,598 workflow INFO:
[Job 90] Completed (preproc.coregwf.applywarp).
180514-10:37:12,601 workflow INFO:
[Job 79] Completed (preproc.datasink).
180514-10:37:12,605 workflow INFO:
[MultiProc] Running 5 tasks, and 5 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:12,665 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:37:12,671 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/smooth".180514-10:37:12,674 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-10:37:12,668 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:37:12,682 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
180514-10:37:12,695 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:37:12,700 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:37:12,703 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg180514-10:37:12,713 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:37:12,726 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:37:12,745 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
180514-10:37:12,760 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-8_ssub-06_ses-test_task-fingerfootlips_bold.nii
180514-10:37:12,769 interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:37:12,789 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:37:14,597 workflow INFO:
[Job 78] Completed (preproc.datasink).
180514-10:37:14,616 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:14,711 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/art".
180514-10:37:14,751 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:37:15,485 workflow INFO:
[Node] Finished "preproc.art".
180514-10:37:16,601 workflow INFO:
[Job 93] Completed (preproc.art).
180514-10:37:16,610 workflow INFO:
[MultiProc] Running 7 tasks, and 1 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:16,666 workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles".
180514-10:37:16,694 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:37:16,738 workflow INFO:
[Node] Finished "preproc.selectfiles".
180514-10:37:18,605 workflow INFO:
[Job 144] Completed (preproc.selectfiles).
180514-10:37:18,608 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:18,665 workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat".
180514-10:37:18,684 workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -f 0.50 -R
180514-10:37:20,611 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.bet_anat
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:35,691 workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
180514-10:37:36,625 workflow INFO:
[Job 145] Completed (preproc.coregwf.bet_anat).
180514-10:37:36,634 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:36,709 workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation".
180514-10:37:36,729 workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain.nii.gz
180514-10:37:38,631 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:57,437 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:37:58,648 workflow INFO:
[Job 92] Completed (preproc.smooth).
180514-10:37:58,656 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:37:58,725 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:37:58,745 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:37:58,758 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-4_ssub-05_ses-test_task-fingerfootlips_bold.nii
180514-10:37:58,771 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
180514-10:37:58,784 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:37:58,797 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
180514-10:37:58,810 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:37:58,823 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
180514-10:37:58,837 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:37:58,855 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:38:00,653 workflow INFO:
[Job 95] Completed (preproc.datasink).
180514-10:38:00,661 workflow INFO:
[MultiProc] Running 7 tasks, and 1 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:00,720 workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract".
180514-10:38:00,735 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:38:01,504 workflow INFO:
[Node] Finished "preproc.extract".
180514-10:38:02,656 workflow INFO:
[Job 148] Completed (preproc.extract).
180514-10:38:02,660 workflow INFO:
[MultiProc] Running 7 tasks, and 1 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.segmentation
* preproc.smooth
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:02,720 workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt".
180514-10:38:02,735 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
180514-10:38:04,356 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:38:04,658 workflow INFO:
[Job 91] Completed (preproc.smooth).
180514-10:38:04,665 workflow INFO:
[MultiProc] Running 7 tasks, and 1 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:04,772 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:38:04,807 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:38:04,838 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
180514-10:38:04,870 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:38:04,894 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
180514-10:38:04,921 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:38:04,945 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
180514-10:38:04,969 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-8_ssub-05_ses-test_task-fingerfootlips_bold.nii
180514-10:38:05,2 interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:38:05,45 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:38:06,670 workflow INFO:
[Job 94] Completed (preproc.datasink).
180514-10:38:06,677 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:35,365 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:38:36,695 workflow INFO:
[Job 133] Completed (preproc.mcflirt).
180514-10:38:36,700 workflow INFO:
[MultiProc] Running 6 tasks, and 2 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:36,768 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre".180514-10:38:36,771 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer".
180514-10:38:36,781 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000180514-10:38:36,787 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:38:38,696 workflow INFO:
[MultiProc] Running 8 tasks, and 0 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:39,111 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:38:40,698 workflow INFO:
[Job 117] Completed (preproc.mcflirt).
180514-10:38:40,706 workflow INFO:
[MultiProc] Running 7 tasks, and 2 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:40,769 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre".
180514-10:38:40,786 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:38:42,703 workflow INFO:
[MultiProc] Running 8 tasks, and 1 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:43,506 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:38:44,703 workflow INFO:
[Job 137] Completed (preproc.slicetimer).
180514-10:38:44,707 workflow INFO:
[MultiProc] Running 7 tasks, and 1 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:44,776 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer".
180514-10:38:44,792 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:38:46,708 workflow INFO:
[MultiProc] Running 8 tasks, and 0 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:38:51,615 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:38:52,677 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:38:52,712 workflow INFO:
[Job 114] Completed (preproc.coregwf.segmentation).
180514-10:38:52,714 workflow INFO:
[Job 121] Completed (preproc.slicetimer).
180514-10:38:52,718 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:38:52,767 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold".
180514-10:38:52,775 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:38:54,4 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:38:54,380 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:38:54,713 workflow INFO:
[Job 134] Completed (preproc.coregwf.coreg_pre).
180514-10:38:54,716 workflow INFO:
[Job 115] Completed (preproc.coregwf.threshold).
180514-10:38:54,719 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
180514-10:38:55,117 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:38:55,703 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:38:56,715 workflow INFO:
[Job 103] Completed (preproc.coregwf.coreg_bbr).
180514-10:38:56,717 workflow INFO:
[Job 118] Completed (preproc.coregwf.coreg_pre).
180514-10:38:56,721 workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:38:56,769 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp_mean".
180514-10:38:56,772 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp".
180514-10:38:56,777 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline180514-10:38:56,778 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr".
180514-10:38:56,785 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:38:56,799 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:38:58,719 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:38:59,886 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:39:00,720 workflow INFO:
[Job 104] Completed (preproc.coregwf.applywarp_mean).
180514-10:39:00,723 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:14,440 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:39:14,734 workflow INFO:
[Job 106] Completed (preproc.coregwf.applywarp).
180514-10:39:14,737 workflow INFO:
[MultiProc] Running 4 tasks, and 3 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:14,786 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:39:14,789 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:39:14,792 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")180514-10:39:14,792 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/art".
180514-10:39:14,800 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
180514-10:39:14,796 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:39:15,533 workflow INFO:
[Node] Finished "preproc.art".
180514-10:39:16,734 workflow INFO:
[Job 109] Completed (preproc.art).
180514-10:39:16,740 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:49,340 workflow INFO:
[Node] Finished "preproc.mcflirt".
180514-10:39:50,766 workflow INFO:
[Job 149] Completed (preproc.mcflirt).
180514-10:39:50,771 workflow INFO:
[MultiProc] Running 5 tasks, and 2 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:50,833 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre".
180514-10:39:50,837 workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer".
180514-10:39:50,846 workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
180514-10:39:50,849 workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
180514-10:39:52,771 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:56,629 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:39:56,773 workflow INFO:
[Job 107] Completed (preproc.smooth).
180514-10:39:56,777 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:56,834 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:39:56,843 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:39:56,851 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
180514-10:39:56,862 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:39:56,866 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
180514-10:39:56,873 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:39:56,879 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
180514-10:39:56,883 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-8_ssub-04_ses-test_task-fingerfootlips_bold.nii
180514-10:39:56,888 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:39:56,902 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:39:57,316 workflow INFO:
[Node] Finished "preproc.slicetimer".
180514-10:39:57,611 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:39:58,775 workflow INFO:
[Job 108] Completed (preproc.smooth).
180514-10:39:58,777 workflow INFO:
[Job 153] Completed (preproc.slicetimer).
180514-10:39:58,779 workflow INFO:
[Job 110] Completed (preproc.datasink).
180514-10:39:58,783 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:39:58,838 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:39:58,847 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:39:58,850 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-4_ssub-04_ses-test_task-fingerfootlips_bold.nii
180514-10:39:58,853 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
180514-10:39:58,858 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:39:58,861 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
180514-10:39:58,865 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:39:58,871 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
180514-10:39:58,875 interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:39:58,886 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:40:00,777 workflow INFO:
[Job 111] Completed (preproc.datasink).
180514-10:40:00,781 workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:40:02,399 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
180514-10:40:02,779 workflow INFO:
[Job 150] Completed (preproc.coregwf.coreg_pre).
180514-10:40:02,782 workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
* preproc.coregwf.segmentation
180514-10:41:12,647 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:41:12,844 workflow INFO:
[Job 146] Completed (preproc.coregwf.segmentation).
180514-10:41:12,847 workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:41:12,887 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold".
180514-10:41:12,894 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:41:13,657 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:41:14,846 workflow INFO:
[Job 147] Completed (preproc.coregwf.threshold).
180514-10:41:14,849 workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:41:14,892 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr".
180514-10:41:14,900 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:41:16,849 workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:42:26,229 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:42:26,913 workflow INFO:
[Job 119] Completed (preproc.coregwf.coreg_bbr).
180514-10:42:26,916 workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:42:26,960 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp_mean".
180514-10:42:26,963 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp".
180514-10:42:26,969 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:42:26,971 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:42:28,916 workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:42:28,931 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:42:30,916 workflow INFO:
[Job 120] Completed (preproc.coregwf.applywarp_mean).
180514-10:42:30,918 workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:42:37,393 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:42:38,924 workflow INFO:
[Job 122] Completed (preproc.coregwf.applywarp).
180514-10:42:38,927 workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:42:38,971 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/smooth".180514-10:42:38,974 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:42:38,979 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/art".180514-10:42:38,979 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:42:38,986 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
180514-10:42:38,993 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:42:39,618 workflow INFO:
[Node] Finished "preproc.art".
180514-10:42:40,926 workflow INFO:
[Job 125] Completed (preproc.art).
180514-10:42:40,930 workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:43:10,381 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:43:10,956 workflow INFO:
[Job 124] Completed (preproc.smooth).
180514-10:43:10,962 workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:43:11,35 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:43:11,45 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:43:11,51 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-4_ssub-03_ses-test_task-fingerfootlips_bold.nii
180514-10:43:11,55 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
180514-10:43:11,58 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:43:11,66 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
180514-10:43:11,69 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:43:11,74 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
180514-10:43:11,77 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:43:11,84 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:43:12,957 workflow INFO:
[Job 127] Completed (preproc.datasink).
180514-10:43:12,961 workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.smooth
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:43:16,849 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:43:16,960 workflow INFO:
[Job 123] Completed (preproc.smooth).
180514-10:43:16,962 workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
180514-10:43:17,10 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:43:17,21 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:43:17,25 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
180514-10:43:17,28 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:43:17,31 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
180514-10:43:17,34 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:43:17,37 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
180514-10:43:17,40 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-8_ssub-03_ses-test_task-fingerfootlips_bold.nii
180514-10:43:17,43 interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:43:17,49 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:43:17,868 workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
180514-10:43:18,962 workflow INFO:
[Job 130] Completed (preproc.coregwf.segmentation).
180514-10:43:18,963 workflow INFO:
[Job 126] Completed (preproc.datasink).
180514-10:43:18,967 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:43:19,9 workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold".
180514-10:43:19,14 workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:43:20,284 workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
180514-10:43:20,964 workflow INFO:
[Job 131] Completed (preproc.coregwf.threshold).
180514-10:43:20,967 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:43:21,11 workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr".
180514-10:43:21,18 workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
180514-10:43:22,965 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_bbr
180514-10:43:26,456 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:43:26,968 workflow INFO:
[Job 151] Completed (preproc.coregwf.coreg_bbr).
180514-10:43:26,971 workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:43:27,15 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp_mean".
180514-10:43:27,18 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp".
180514-10:43:27,24 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline180514-10:43:27,25 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:43:28,919 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:43:28,970 workflow INFO:
[Job 152] Completed (preproc.coregwf.applywarp_mean).
180514-10:43:28,974 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.coreg_bbr
180514-10:43:37,151 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:43:38,980 workflow INFO:
[Job 154] Completed (preproc.coregwf.applywarp).
180514-10:43:38,984 workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:43:39,28 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:43:39,30 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/smooth".180514-10:43:39,33 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")180514-10:43:39,33 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/art".
180514-10:43:39,36 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:43:39,47 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:43:39,648 workflow INFO:
[Node] Finished "preproc.art".
180514-10:43:40,982 workflow INFO:
[Job 157] Completed (preproc.art).
180514-10:43:40,986 workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
180514-10:44:09,103 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:44:10,301 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:44:11,8 workflow INFO:
[Job 155] Completed (preproc.smooth).
180514-10:44:11,10 workflow INFO:
[Job 156] Completed (preproc.smooth).
180514-10:44:11,14 workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:44:11,63 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:44:11,70 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:44:11,73 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/datasink".180514-10:44:11,74 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
180514-10:44:11,77 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:44:11,81 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
180514-10:44:11,85 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:44:11,87 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:44:11,89 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii
180514-10:44:11,91 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
180514-10:44:11,93 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
180514-10:44:11,95 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii
180514-10:44:11,98 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:44:11,101 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:44:11,106 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:44:11,105 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
180514-10:44:11,117 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:44:11,120 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
180514-10:44:11,123 interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:44:11,130 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:44:13,10 workflow INFO:
[Job 158] Completed (preproc.datasink).
180514-10:44:13,13 workflow INFO:
[Job 159] Completed (preproc.datasink).
180514-10:44:13,16 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.coreg_bbr
180514-10:45:54,984 workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
180514-10:45:55,113 workflow INFO:
[Job 135] Completed (preproc.coregwf.coreg_bbr).
180514-10:45:55,120 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:45:55,167 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp_mean".
180514-10:45:55,170 workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp".
180514-10:45:55,173 workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline180514-10:45:55,179 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
180514-10:45:57,113 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
180514-10:45:58,304 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
180514-10:45:59,114 workflow INFO:
[Job 136] Completed (preproc.coregwf.applywarp_mean).
180514-10:45:59,117 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.coregwf.applywarp
180514-10:46:07,381 workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
180514-10:46:09,127 workflow INFO:
[Job 138] Completed (preproc.coregwf.applywarp).
180514-10:46:09,134 workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:46:09,180 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/smooth".
180514-10:46:09,183 workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/smooth".
180514-10:46:09,186 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")180514-10:46:09,188 workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/art".
180514-10:46:09,190 workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
180514-10:46:09,195 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 117, in _handle_events
handler_func(fileobj, events)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:46:09,805 workflow INFO:
[Node] Finished "preproc.art".
180514-10:46:11,128 workflow INFO:
[Job 141] Completed (preproc.art).
180514-10:46:11,132 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* preproc.smooth
* preproc.smooth
180514-10:46:39,5 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:46:39,154 workflow INFO:
[Job 140] Completed (preproc.smooth).
180514-10:46:39,157 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.smooth
180514-10:46:39,209 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/datasink".
180514-10:46:39,220 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:46:39,225 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-4_ssub-02_ses-test_task-fingerfootlips_bold.nii
180514-10:46:39,228 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
180514-10:46:39,233 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:46:39,237 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
180514-10:46:39,242 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:46:39,245 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
180514-10:46:39,249 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:46:39,258 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:46:41,156 workflow INFO:
[Job 143] Completed (preproc.datasink).
180514-10:46:41,159 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* preproc.smooth
180514-10:46:44,340 workflow INFO:
[Node] Finished "preproc.smooth".
180514-10:46:45,162 workflow INFO:
[Job 139] Completed (preproc.smooth).
180514-10:46:45,171 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:46:45,224 workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/datasink".
180514-10:46:45,234 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:46:45,238 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
180514-10:46:45,242 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
180514-10:46:45,245 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
180514-10:46:45,247 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
180514-10:46:45,250 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
180514-10:46:45,253 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-8_ssub-02_ses-test_task-fingerfootlips_bold.nii
180514-10:46:45,257 interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
180514-10:46:45,266 workflow INFO:
[Node] Finished "preproc.datasink".
180514-10:46:47,164 workflow INFO:
[Job 142] Completed (preproc.datasink).
180514-10:46:47,172 workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
Out[ ]:
<networkx.classes.digraph.DiGraph at 0x7f0c1dbbe0f0>
Inspect output¶
Let's check the structure of the output folder, to see if we have everything we wanted to save.
In [ ]:
!tree /output/datasink/preproc
/output/datasink/preproc
├── sub-01
│ └── task-fingerfootlips
│ ├── art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-01_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-01_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-01_ses-test_task-fingerfootlips_bold.par
│ └── sub-01_t1w_preproc_brain.nii.gz
├── sub-02
│ └── task-fingerfootlips
│ ├── art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-02_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-02_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-02_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-02_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-02_ses-test_task-fingerfootlips_bold.par
│ └── sub-02_t1w_preproc_brain.nii.gz
├── sub-03
│ └── task-fingerfootlips
│ ├── art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-03_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-03_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-03_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-03_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-03_ses-test_task-fingerfootlips_bold.par
│ └── sub-03_t1w_preproc_brain.nii.gz
├── sub-04
│ └── task-fingerfootlips
│ ├── art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-04_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-04_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-04_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-04_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-04_ses-test_task-fingerfootlips_bold.par
│ └── sub-04_t1w_preproc_brain.nii.gz
├── sub-05
│ └── task-fingerfootlips
│ ├── art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-05_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-05_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-05_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-05_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-05_ses-test_task-fingerfootlips_bold.par
│ └── sub-05_t1w_preproc_brain.nii.gz
├── sub-06
│ └── task-fingerfootlips
│ ├── art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-06_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-06_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-06_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-06_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-06_ses-test_task-fingerfootlips_bold.par
│ └── sub-06_t1w_preproc_brain.nii.gz
├── sub-07
│ └── task-fingerfootlips
│ ├── art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-07_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-07_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-07_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-07_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-07_ses-test_task-fingerfootlips_bold.par
│ └── sub-07_t1w_preproc_brain.nii.gz
├── sub-08
│ └── task-fingerfootlips
│ ├── art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-08_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-08_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-08_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-08_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-08_ses-test_task-fingerfootlips_bold.par
│ └── sub-08_t1w_preproc_brain.nii.gz
├── sub-09
│ └── task-fingerfootlips
│ ├── art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-09_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-09_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-09_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-09_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-09_ses-test_task-fingerfootlips_bold.par
│ └── sub-09_t1w_preproc_brain.nii.gz
└── sub-10
└── task-fingerfootlips
├── art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
├── fwhm-4_ssub-10_ses-test_task-fingerfootlips_bold.nii
├── fwhm-8_ssub-10_ses-test_task-fingerfootlips_bold.nii
├── plot.sub-10_ses-test_task-fingerfootlips_bold.svg
├── sub-10_ses-test_task-fingerfootlips_bold_mean.mat
├── sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
├── sub-10_ses-test_task-fingerfootlips_bold.par
└── sub-10_t1w_preproc_brain.nii.gz
20 directories, 80 files
Visualize results¶
Let's check the effect of the different smoothing kernels.
In [ ]:
from nilearn import image, plotting
%matplotlib inline
out_path = '/output/datasink/preproc/sub-01/task-fingerfootlips'
In [ ]:
plotting.plot_epi(
'/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz',
title="T1", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
In [ ]:
plotting.plot_epi(opj(out_path, 'sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz'),
title="fwhm = 0mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
In [ ]:
plotting.plot_epi(image.mean_img(opj(out_path, 'fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii')),
title="fwhm = 4mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
In [ ]:
plotting.plot_epi(image.mean_img(opj(out_path, 'fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii')),
title="fwhm = 8mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
Now, let's investigate the motion parameters. How much did the subject move and turn in the scanner?
In [ ]:
import numpy as np
import pylab as plt
par = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par')
fig, axes = plt.subplots(2, 1, figsize=(15, 5))
axes[0].set_ylabel('rotation (radians)')
axes[0].plot(par[0:, :3])
axes[1].plot(par[0:, 3:])
axes[1].set_xlabel('time (TR)')
axes[1].set_ylabel('translation (mm)');
There seems to be a rather drastic motion around volume 102. Let's check if the outliers detection algorithm was able to pick this up.
In [ ]:
import numpy as np
outlier_ids = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt')
print('Outliers were detected at volumes: %s' % outlier_ids)
from IPython.display import SVG
SVG(filename='/output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg')
Outliers were detected at volumes: [ 59. 102.]
Out[ ]: