Example 4: 2nd-level Analysis¶
Last but not least, the 2nd-level analysis. After we removed left-handed subjects and normalized all subject data into template space, we can now do the group analysis. To show the flexibility of Nipype, we will run the group analysis on data with two different smoothing kernel (fwhm= [4, 8]) and two different normalizations (ANTs and SPM).
This example will also directly include thresholding of the output, as well as some visualization.
Let's start!
In [ ]:
%matplotlib inline
from os.path import join as opj
from nipype.interfaces.io import SelectFiles, DataSink
from nipype.interfaces.spm import (OneSampleTTestDesign, EstimateModel,
EstimateContrast, Threshold)
from nipype.interfaces.utility import IdentityInterface
from nipype import Workflow, Node
from nipype.interfaces.fsl import Info
from nipype.algorithms.misc import Gunzip
Experiment parameters (SPM12)¶
It's always a good idea to specify all parameters that might change between experiments at the beginning of your script.
In [ ]:
experiment_dir = '/output'
output_dir = 'datasink'
working_dir = 'workingdir'
# Smoothing withds used during preprocessing
fwhm = [4, 8]
# Which contrasts to use for the 2nd-level analysis
contrast_list = ['con_0001', 'con_0002', 'con_0003', 'con_0004', 'con_0005', 'con_0006', 'con_0007']
mask = "/data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c/1mm_brainmask.nii.gz"
Specify Nodes (SPM12)¶
Initiate all the different interfaces (represented as nodes) that you want to use in your workflow.
In [ ]:
# Gunzip - unzip the mask image
gunzip = Node(Gunzip(in_file=mask), name="gunzip")
# OneSampleTTestDesign - creates one sample T-Test Design
onesamplettestdes = Node(OneSampleTTestDesign(),
name="onesampttestdes")
# EstimateModel - estimates the model
level2estimate = Node(EstimateModel(estimation_method={'Classical': 1}),
name="level2estimate")
# EstimateContrast - estimates group contrast
level2conestimate = Node(EstimateContrast(group_contrast=True),
name="level2conestimate")
cont1 = ['Group', 'T', ['mean'], [1]]
level2conestimate.inputs.contrasts = [cont1]
# Threshold - thresholds contrasts
level2thresh = Node(Threshold(contrast_index=1,
use_topo_fdr=True,
use_fwe_correction=False,
extent_threshold=0,
height_threshold=0.005,
height_threshold_type='p-value',
extent_fdr_p_threshold=0.05),
name="level2thresh")
Specify input & output stream (SPM12)¶
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=['contrast_id', 'fwhm_id']),
name="infosource")
infosource.iterables = [('contrast_id', contrast_list),
('fwhm_id', fwhm)]
# SelectFiles - to grab the data (alternativ to DataGrabber)
templates = {'cons': opj(output_dir, 'norm_spm', 'sub-*_fwhm{fwhm_id}',
'w{contrast_id}.nii')}
selectfiles = Node(SelectFiles(templates,
base_directory=experiment_dir,
sort_filelist=True),
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 = [('_contrast_id_', '')]
subjFolders = [('%s_fwhm_id_%s' % (con, f), 'spm_%s_fwhm%s' % (con, f))
for f in fwhm
for con in contrast_list]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
Specify Workflow (SPM12)¶
Create a workflow and connect the interface nodes and the I/O stream to each other.
In [ ]:
# Initiation of the 2nd-level analysis workflow
l2analysis = Workflow(name='spm_l2analysis')
l2analysis.base_dir = opj(experiment_dir, working_dir)
# Connect up the 2nd-level analysis components
l2analysis.connect([(infosource, selectfiles, [('contrast_id', 'contrast_id'),
('fwhm_id', 'fwhm_id')]),
(selectfiles, onesamplettestdes, [('cons', 'in_files')]),
(gunzip, onesamplettestdes, [('out_file',
'explicit_mask_file')]),
(onesamplettestdes, level2estimate, [('spm_mat_file',
'spm_mat_file')]),
(level2estimate, level2conestimate, [('spm_mat_file',
'spm_mat_file'),
('beta_images',
'beta_images'),
('residual_image',
'residual_image')]),
(level2conestimate, level2thresh, [('spm_mat_file',
'spm_mat_file'),
('spmT_images',
'stat_image'),
]),
(level2conestimate, datasink, [('spm_mat_file',
'2ndLevel.@spm_mat'),
('spmT_images',
'2ndLevel.@T'),
('con_images',
'2ndLevel.@con')]),
(level2thresh, datasink, [('thresholded_map',
'2ndLevel.@threshold')]),
])
Visualize the workflow (SPM12)¶
It always helps to visualize your workflow.
In [ ]:
# Create 1st-level analysis output graph
l2analysis.write_graph(graph2use='colored', format='png', simple_form=True)
# Visualize the graph
from IPython.display import Image
Image(filename=opj(l2analysis.base_dir, 'spm_l2analysis', 'graph.png'))
180514-11:11:37,49 workflow INFO: Generated workflow graph: /output/workingdir/spm_l2analysis/graph.png (graph2use=colored, simple_form=True).
Out[ ]:
Run the Workflow (SPM12)¶
Now that everything is ready, we can run the 1st-level analysis workflow. Change n_procs to the number of jobs/cores you want to use.
In [ ]:
l2analysis.run('MultiProc', plugin_args={'n_procs': 8})
180514-11:11:37,120 workflow INFO:
Workflow spm_l2analysis settings: ['check', 'execution', 'logging', 'monitoring']
180514-11:11:37,206 workflow INFO:
Running in parallel.
180514-11:11:37,211 workflow INFO:
[MultiProc] Running 0 tasks, and 15 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:11:37,272 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/selectfiles".180514-11:11:37,274 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/selectfiles".
180514-11:11:37,281 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:37,283 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:37,284 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/selectfiles".
180514-11:11:37,287 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/selectfiles".
180514-11:11:37,296 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:11:37,296 workflow INFO:
[Node] Finished "spm_l2analysis.selectfiles".
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[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/selectfiles".
180514-11:11:37,276 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/selectfiles".180514-11:11:37,282 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/selectfiles".
180514-11:11:37,307 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
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[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:11:37,313 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:37,300 workflow INFO:
[Node] Finished "spm_l2analysis.selectfiles".180514-11:11:37,319 workflow INFO:
[Node] Finished "spm_l2analysis.selectfiles".
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[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:37,282 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/selectfiles".
180514-11:11:37,329 workflow INFO:
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[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
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[Node] Finished "spm_l2analysis.selectfiles".
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[Job 0] Completed (spm_l2analysis.selectfiles).
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[MultiProc] Running 0 tasks, and 7 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:11:39,282 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/selectfiles".
180514-11:11:39,284 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/selectfiles".
180514-11:11:39,288 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:11:39,289 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/selectfiles".180514-11:11:39,291 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:39,292 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/selectfiles".180514-11:11:39,295 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/selectfiles".
180514-11:11:39,297 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:11:39,299 workflow INFO:
[Node] Setting-up "spm_l2analysis.selectfiles" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/selectfiles".
180514-11:11:39,300 workflow INFO:
[Node] Finished "spm_l2analysis.selectfiles".
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[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
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[Node] Setting-up "spm_l2analysis.gunzip" in "/output/workingdir/spm_l2analysis/gunzip".180514-11:11:39,306 workflow INFO:
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[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
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[Node] Running "gunzip" ("nipype.algorithms.misc.Gunzip")180514-11:11:39,316 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:11:39,317 workflow INFO:
[Node] Finished "spm_l2analysis.selectfiles".
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[Job 8] Completed (spm_l2analysis.selectfiles).
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[MultiProc] Running 0 tasks, and 14 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:11:41,345 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/onesampttestdes".
180514-11:11:41,350 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/onesampttestdes".
180514-11:11:41,352 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:41,354 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/onesampttestdes".180514-11:11:41,359 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:11:41,358 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/onesampttestdes".
180514-11:11:41,360 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:41,366 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/onesampttestdes".180514-11:11:41,367 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:41,375 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/onesampttestdes".180514-11:11:41,382 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/onesampttestdes".
180514-11:11:41,373 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:41,388 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:11:41,390 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/onesampttestdes".
180514-11:11:41,395 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:41,401 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:11:43,222 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:12:11,657 workflow INFO:
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[MultiProc] Running 0 tasks, and 14 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
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[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2estimate".
180514-11:12:13,325 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2estimate".
180514-11:12:13,328 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:12:13,330 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:12:13,328 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2estimate".180514-11:12:13,331 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2estimate".
180514-11:12:13,334 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2estimate".
180514-11:12:13,339 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:12:13,337 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2estimate".
180514-11:12:13,345 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:12:13,342 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2estimate".
180514-11:12:13,352 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2estimate".
180514-11:12:13,340 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
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[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:12:13,392 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:12:13,391 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
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[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
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Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
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[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2conestimate".
180514-11:12:49,369 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2conestimate".
180514-11:12:49,376 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2conestimate".180514-11:12:49,378 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:49,384 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2conestimate".180514-11:12:49,385 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:49,396 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:49,402 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:49,427 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:12:51,296 workflow INFO:
[Job 16] Completed (spm_l2analysis.level2estimate).
180514-11:12:51,299 workflow INFO:
[Job 31] Completed (spm_l2analysis.level2estimate).
180514-11:12:51,303 workflow INFO:
[Job 36] Completed (spm_l2analysis.level2estimate).
180514-11:12:51,305 workflow INFO:
[Job 51] Completed (spm_l2analysis.level2estimate).
180514-11:12:51,310 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:12:51,364 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2conestimate".
180514-11:12:51,370 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2conestimate".180514-11:12:51,375 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2conestimate".
180514-11:12:51,389 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:12:51,388 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2conestimate".
180514-11:12:51,410 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:12:51,415 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:51,430 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:12:53,303 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:13:11,434 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:11,481 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:11,599 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:13,153 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:13,320 workflow INFO:
[Job 22] Completed (spm_l2analysis.level2conestimate).
180514-11:13:13,325 workflow INFO:
[Job 27] Completed (spm_l2analysis.level2conestimate).
180514-11:13:13,330 workflow INFO:
[Job 42] Completed (spm_l2analysis.level2conestimate).
180514-11:13:13,337 workflow INFO:
[Job 47] Completed (spm_l2analysis.level2conestimate).
180514-11:13:13,347 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:13:13,404 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2thresh".
180514-11:13:13,409 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2thresh".180514-11:13:13,411 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2thresh".
180514-11:13:13,415 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2thresh".180514-11:13:13,417 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:13,425 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:13:13,426 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:13,437 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:14,119 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:14,243 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:14,409 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:14,424 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:13:15,320 workflow INFO:
[Job 17] Completed (spm_l2analysis.level2conestimate).
180514-11:13:15,323 workflow INFO:
[Job 32] Completed (spm_l2analysis.level2conestimate).
180514-11:13:15,325 workflow INFO:
[Job 37] Completed (spm_l2analysis.level2conestimate).
180514-11:13:15,328 workflow INFO:
[Job 52] Completed (spm_l2analysis.level2conestimate).
180514-11:13:15,332 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:13:15,387 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2thresh".
180514-11:13:15,392 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2thresh".
180514-11:13:15,397 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2thresh".180514-11:13:15,402 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2thresh".
180514-11:13:15,405 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:15,403 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:15,429 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:13:15,419 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:13:17,324 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:13:25,26 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:25,60 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:25,67 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:25,155 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:25,331 workflow INFO:
[Job 23] Completed (spm_l2analysis.level2thresh).
180514-11:13:25,337 workflow INFO:
[Job 28] Completed (spm_l2analysis.level2thresh).
180514-11:13:25,342 workflow INFO:
[Job 43] Completed (spm_l2analysis.level2thresh).
180514-11:13:25,349 workflow INFO:
[Job 48] Completed (spm_l2analysis.level2thresh).
180514-11:13:25,357 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:13:25,456 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/datasink".
180514-11:13:25,464 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/datasink".180514-11:13:25,465 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:13:25,470 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm4/spmT_0001_thr.nii
180514-11:13:25,474 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:13:25,475 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/datasink".
180514-11:13:25,478 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0007_fwhm4/SPM.mat
180514-11:13:25,478 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm8/spmT_0001_thr.nii
180514-11:13:25,480 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm4/spmT_0001.nii
180514-11:13:25,483 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm4/con_0001.nii180514-11:13:25,484 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/datasink".
180514-11:13:25,488 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:13:25,480 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0006_fwhm8/SPM.mat
180514-11:13:25,491 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm8/spmT_0001.nii180514-11:13:25,492 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001_thr.nii
180514-11:13:25,493 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:25,496 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm8/con_0001.nii
180514-11:13:25,503 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:25,509 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0005_fwhm4/SPM.mat
180514-11:13:25,512 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001.nii
180514-11:13:25,514 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:13:25,516 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm4/con_0001.nii
180514-11:13:25,519 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm8/spmT_0001_thr.nii
180514-11:13:25,523 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0004_fwhm8/SPM.mat180514-11:13:25,523 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:25,526 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm8/spmT_0001.nii
180514-11:13:25,529 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm8/con_0001.nii
180514-11:13:25,535 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:26,993 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:27,58 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:27,138 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:27,206 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:13:27,334 workflow INFO:
[Job 18] Completed (spm_l2analysis.level2thresh).
180514-11:13:27,340 workflow INFO:
[Job 33] Completed (spm_l2analysis.level2thresh).
180514-11:13:27,346 workflow INFO:
[Job 38] Completed (spm_l2analysis.level2thresh).
180514-11:13:27,353 workflow INFO:
[Job 53] Completed (spm_l2analysis.level2thresh).
180514-11:13:27,360 workflow INFO:
[Job 24] Completed (spm_l2analysis.datasink).
180514-11:13:27,366 workflow INFO:
[Job 29] Completed (spm_l2analysis.datasink).
180514-11:13:27,370 workflow INFO:
[Job 44] Completed (spm_l2analysis.datasink).
180514-11:13:27,373 workflow INFO:
[Job 49] Completed (spm_l2analysis.datasink).
180514-11:13:27,376 workflow INFO:
[MultiProc] Running 0 tasks, and 10 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:13:27,431 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/datasink".
180514-11:13:27,438 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:13:27,440 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/datasink".
180514-11:13:27,442 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm8/spmT_0001_thr.nii180514-11:13:27,450 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:13:27,451 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/datasink".
180514-11:13:27,455 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm4/spmT_0001_thr.nii180514-11:13:27,454 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0007_fwhm8/SPM.mat
180514-11:13:27,459 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm8/spmT_0001.nii180514-11:13:27,463 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0006_fwhm4/SPM.mat180514-11:13:27,460 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:13:27,463 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0007_fwhm8/con_0001.nii
180514-11:13:27,466 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm4/spmT_0001.nii180514-11:13:27,466 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001_thr.nii
180514-11:13:27,470 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".180514-11:13:27,470 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0005_fwhm8/SPM.mat180514-11:13:27,472 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/onesampttestdes".180514-11:13:27,470 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0006_fwhm4/con_0001.nii180514-11:13:27,473 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/datasink".
180514-11:13:27,481 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:13:27,481 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:27,483 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:13:27,479 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/onesampttestdes".
180514-11:13:27,486 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/onesampttestdes".
180514-11:13:27,489 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001.nii180514-11:13:27,492 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:13:27,492 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:13:27,493 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/onesampttestdes".
180514-11:13:27,502 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0005_fwhm8/con_0001.nii
180514-11:13:27,506 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:13:27,507 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm4/spmT_0001_thr.nii180514-11:13:27,514 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:27,527 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0004_fwhm4/SPM.mat
180514-11:13:27,533 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm4/spmT_0001.nii
180514-11:13:27,537 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0004_fwhm4/con_0001.nii
180514-11:13:27,547 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:13:29,334 workflow INFO:
[Job 19] Completed (spm_l2analysis.datasink).
180514-11:13:29,338 workflow INFO:
[Job 34] Completed (spm_l2analysis.datasink).
180514-11:13:29,342 workflow INFO:
[Job 39] Completed (spm_l2analysis.datasink).
180514-11:13:29,345 workflow INFO:
[Job 54] Completed (spm_l2analysis.datasink).
180514-11:13:29,351 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:13:29,402 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/onesampttestdes".
180514-11:13:29,410 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/onesampttestdes".
180514-11:13:29,421 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:13:29,416 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:13:31,340 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:13:44,299 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:44,702 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:44,808 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:44,917 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:45,352 workflow INFO:
[Job 55] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:45,357 workflow INFO:
[Job 60] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:45,363 workflow INFO:
[Job 65] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:45,365 workflow INFO:
[Job 70] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:45,368 workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:13:45,410 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2estimate".
180514-11:13:45,413 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2estimate".180514-11:13:45,415 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:13:45,417 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2estimate".
180514-11:13:45,423 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2estimate".180514-11:13:45,421 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:13:45,425 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:13:45,429 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:13:46,801 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:47,352 workflow INFO:
[Job 75] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:47,355 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.onesampttestdes
180514-11:13:47,359 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:13:47,415 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2estimate".
180514-11:13:47,446 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:13:49,355 workflow INFO:
[Job 80] Completed (spm_l2analysis.onesampttestdes).
180514-11:13:49,359 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:13:49,422 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2estimate".
180514-11:13:49,446 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:13:51,358 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:14:11,769 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:12,601 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:12,667 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:12,690 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:13,372 workflow INFO:
[Job 56] Completed (spm_l2analysis.level2estimate).
180514-11:14:13,375 workflow INFO:
[Job 61] Completed (spm_l2analysis.level2estimate).
180514-11:14:13,377 workflow INFO:
[Job 66] Completed (spm_l2analysis.level2estimate).
180514-11:14:13,380 workflow INFO:
[Job 71] Completed (spm_l2analysis.level2estimate).
180514-11:14:13,383 workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:14:13,430 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2conestimate".
180514-11:14:13,437 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2conestimate".
180514-11:14:13,444 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:14:13,444 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2conestimate".
180514-11:14:13,454 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2conestimate".
180514-11:14:13,460 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:14:13,458 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:14:13,471 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:14:15,338 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:15,374 workflow INFO:
[Job 76] Completed (spm_l2analysis.level2estimate).
180514-11:14:15,377 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2estimate
180514-11:14:15,436 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2conestimate".
180514-11:14:15,451 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:14:16,570 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:14:17,376 workflow INFO:
[Job 81] Completed (spm_l2analysis.level2estimate).
180514-11:14:17,380 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:14:17,439 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2conestimate".
180514-11:14:17,457 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:14:19,380 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:14:32,78 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:32,422 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:32,501 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:32,567 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:33,392 workflow INFO:
[Job 57] Completed (spm_l2analysis.level2conestimate).
180514-11:14:33,396 workflow INFO:
[Job 62] Completed (spm_l2analysis.level2conestimate).
180514-11:14:33,398 workflow INFO:
[Job 67] Completed (spm_l2analysis.level2conestimate).
180514-11:14:33,400 workflow INFO:
[Job 72] Completed (spm_l2analysis.level2conestimate).
180514-11:14:33,402 workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:14:33,467 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2thresh".
180514-11:14:33,472 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2thresh".
180514-11:14:33,477 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2thresh".
180514-11:14:33,480 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:14:33,481 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2thresh".
180514-11:14:33,489 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:14:33,495 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:14:33,493 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:14:34,991 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:35,394 workflow INFO:
[Job 77] Completed (spm_l2analysis.level2conestimate).
180514-11:14:35,398 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2conestimate
180514-11:14:35,449 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2thresh".
180514-11:14:35,474 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:14:35,893 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:14:37,397 workflow INFO:
[Job 82] Completed (spm_l2analysis.level2conestimate).
180514-11:14:37,403 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:14:37,486 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2thresh".
180514-11:14:37,511 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:14:39,399 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:14:43,196 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:43,300 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:43,403 workflow INFO:
[Job 58] Completed (spm_l2analysis.level2thresh).
180514-11:14:43,407 workflow INFO:
[Job 73] Completed (spm_l2analysis.level2thresh).
180514-11:14:43,411 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:14:43,457 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:43,496 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/datasink".
180514-11:14:43,506 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:14:43,506 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/datasink".
180514-11:14:43,519 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:14:43,520 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm8/spmT_0001_thr.nii
180514-11:14:43,527 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0003_fwhm8/SPM.mat180514-11:14:43,527 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm4/spmT_0001_thr.nii
180514-11:14:43,534 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm8/spmT_0001.nii180514-11:14:43,534 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0002_fwhm4/SPM.mat
180514-11:14:43,538 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm8/con_0001.nii
180514-11:14:43,547 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".180514-11:14:43,541 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm4/spmT_0001.nii
180514-11:14:43,555 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm4/con_0001.nii
180514-11:14:43,573 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:14:45,404 workflow INFO:
[Job 63] Completed (spm_l2analysis.level2thresh).
180514-11:14:45,408 workflow INFO:
[Job 59] Completed (spm_l2analysis.datasink).
180514-11:14:45,409 workflow INFO:
[Job 74] Completed (spm_l2analysis.datasink).
180514-11:14:45,412 workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:14:45,484 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/datasink".
180514-11:14:45,491 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:14:45,495 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm4/spmT_0001_thr.nii
180514-11:14:45,498 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0003_fwhm4/SPM.mat
180514-11:14:45,502 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm4/spmT_0001.nii
180514-11:14:45,505 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0003_fwhm4/con_0001.nii
180514-11:14:45,510 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:14:45,834 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:47,407 workflow INFO:
[Job 78] Completed (spm_l2analysis.level2thresh).
180514-11:14:47,411 workflow INFO:
[Job 64] Completed (spm_l2analysis.datasink).
180514-11:14:47,415 workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:14:47,490 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/datasink".
180514-11:14:47,499 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:14:47,504 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm8/spmT_0001_thr.nii
180514-11:14:47,507 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0001_fwhm8/SPM.mat
180514-11:14:47,510 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm8/spmT_0001.nii
180514-11:14:47,514 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm8/con_0001.nii
180514-11:14:47,527 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:14:48,762 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:49,408 workflow INFO:
[Job 68] Completed (spm_l2analysis.level2thresh).
180514-11:14:49,409 workflow INFO:
[Job 79] Completed (spm_l2analysis.datasink).
180514-11:14:49,412 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* spm_l2analysis.level2thresh
180514-11:14:49,464 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/datasink".
180514-11:14:49,474 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:14:49,478 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm8/spmT_0001_thr.nii
180514-11:14:49,484 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/spm_con_0002_fwhm8/SPM.mat
180514-11:14:49,487 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm8/spmT_0001.nii
180514-11:14:49,493 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0002_fwhm8/con_0001.nii
180514-11:14:49,500 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:14:51,414 workflow INFO:
[Job 69] Completed (spm_l2analysis.datasink).
180514-11:14:51,418 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* spm_l2analysis.level2thresh
180514-11:14:52,506 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:14:53,414 workflow INFO:
[Job 83] Completed (spm_l2analysis.level2thresh).
180514-11:14:53,422 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:14:53,472 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/datasink".
180514-11:14:53,480 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:14:53,483 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm4/spmT_0001_thr.nii
180514-11:14:53,486 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/spm_con_0001_fwhm4/SPM.mat
180514-11:14:53,489 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm4/spmT_0001.nii
180514-11:14:53,494 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/spm_con_0001_fwhm4/con_0001.nii
180514-11:14:53,501 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:14:55,417 workflow INFO:
[Job 84] Completed (spm_l2analysis.datasink).
180514-11:14:55,424 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 0x7f665c4400f0>
Group Analysis with ANTs¶
Now to run the same group analysis, but on the ANTs normalized images, we just need to change a few parameters:
In [ ]:
# Change the SelectFiles template and recreate the node
templates = {'cons': opj(output_dir, 'norm_ants', 'sub-*_fwhm{fwhm_id}',
'{contrast_id}_trans.nii')}
selectfiles = Node(SelectFiles(templates,
base_directory=experiment_dir,
sort_filelist=True),
name="selectfiles")
# Change the substituion parameters for the datasink
substitutions = [('_contrast_id_', '')]
subjFolders = [('%s_fwhm_id_%s' % (con, f), 'ants_%s_fwhm%s' % (con, f))
for f in fwhm
for con in contrast_list]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
Now, we just have to recreate the workflow.
In [ ]:
# Initiation of the 2nd-level analysis workflow
l2analysis = Workflow(name='ants_l2analysis')
l2analysis.base_dir = opj(experiment_dir, working_dir)
# Connect up the 2nd-level analysis components
l2analysis.connect([(infosource, selectfiles, [('contrast_id', 'contrast_id'),
('fwhm_id', 'fwhm_id')]),
(selectfiles, onesamplettestdes, [('cons', 'in_files')]),
(gunzip, onesamplettestdes, [('out_file',
'explicit_mask_file')]),
(onesamplettestdes, level2estimate, [('spm_mat_file',
'spm_mat_file')]),
(level2estimate, level2conestimate, [('spm_mat_file',
'spm_mat_file'),
('beta_images',
'beta_images'),
('residual_image',
'residual_image')]),
(level2conestimate, level2thresh, [('spm_mat_file',
'spm_mat_file'),
('spmT_images',
'stat_image'),
]),
(level2conestimate, datasink, [('spm_mat_file',
'2ndLevel.@spm_mat'),
('spmT_images',
'2ndLevel.@T'),
('con_images',
'2ndLevel.@con')]),
(level2thresh, datasink, [('thresholded_map',
'2ndLevel.@threshold')]),
])
And we can run it!
In [ ]:
l2analysis.run('MultiProc', plugin_args={'n_procs': 8})
180514-11:14:57,531 workflow INFO:
Workflow ants_l2analysis settings: ['check', 'execution', 'logging', 'monitoring']
180514-11:14:57,624 workflow INFO:
Running in parallel.
180514-11:14:57,629 workflow INFO:
[MultiProc] Running 0 tasks, and 15 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:14:57,691 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0007_fwhm_id_8/selectfiles".
180514-11:14:57,697 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0006_fwhm_id_4/selectfiles".180514-11:14:57,696 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0007_fwhm_id_4/selectfiles".180514-11:14:57,697 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0006_fwhm_id_8/selectfiles".180514-11:14:57,699 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0005_fwhm_id_8/selectfiles".
180514-11:14:57,701 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:57,707 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:57,701 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0005_fwhm_id_4/selectfiles".180514-11:14:57,707 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:57,713 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:57,716 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:57,709 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0004_fwhm_id_8/selectfiles".180514-11:14:57,707 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:57,712 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0004_fwhm_id_4/selectfiles".180514-11:14:57,725 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:57,726 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:57,737 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:57,735 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:57,737 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".180514-11:14:57,727 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".180514-11:14:57,739 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:57,747 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".180514-11:14:57,749 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:57,758 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:59,636 workflow INFO:
[Job 0] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,642 workflow INFO:
[Job 1] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,647 workflow INFO:
[Job 2] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,649 workflow INFO:
[Job 3] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,650 workflow INFO:
[Job 4] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,653 workflow INFO:
[Job 5] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,654 workflow INFO:
[Job 6] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,656 workflow INFO:
[Job 7] Completed (ants_l2analysis.selectfiles).
180514-11:14:59,660 workflow INFO:
[MultiProc] Running 0 tasks, and 7 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:14:59,705 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0003_fwhm_id_8/selectfiles".
180514-11:14:59,706 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0003_fwhm_id_4/selectfiles".
180514-11:14:59,708 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0002_fwhm_id_8/selectfiles".180514-11:14:59,716 workflow INFO:
[Job 14] Cached (spm_l2analysis.gunzip).
180514-11:14:59,710 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0002_fwhm_id_4/selectfiles".180514-11:14:59,711 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:59,711 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0001_fwhm_id_8/selectfiles".
180514-11:14:59,714 workflow INFO:
[Node] Setting-up "ants_l2analysis.selectfiles" in "/output/workingdir/ants_l2analysis/_contrast_id_con_0001_fwhm_id_4/selectfiles".
180514-11:14:59,718 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:59,720 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:59,718 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:59,714 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-11:14:59,722 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:59,727 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:59,734 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".180514-11:14:59,732 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:59,715 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-11:14:59,733 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:14:59,751 workflow INFO:
[Node] Finished "ants_l2analysis.selectfiles".
180514-11:15:01,638 workflow INFO:
[Job 8] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,645 workflow INFO:
[Job 9] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,652 workflow INFO:
[Job 10] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,654 workflow INFO:
[Job 11] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,656 workflow INFO:
[Job 12] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,658 workflow INFO:
[Job 13] Completed (ants_l2analysis.selectfiles).
180514-11:15:01,660 workflow INFO:
[MultiProc] Running 0 tasks, and 14 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:15:01,708 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,713 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/onesampttestdes".
180514-11:15:01,716 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,716 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,720 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/onesampttestdes".180514-11:15:01,723 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,723 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:15:01,725 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,730 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,729 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/onesampttestdes".
180514-11:15:01,733 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:15:01,736 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/onesampttestdes".180514-11:15:01,734 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".180514-11:15:01,738 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,740 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,746 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,744 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/onesampttestdes".180514-11:15:01,750 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:15:01,752 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,754 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:15:01,756 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".180514-11:15:01,756 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/onesampttestdes".
180514-11:15:01,760 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/onesampttestdes".180514-11:15:01,761 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,763 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,765 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".180514-11:15:01,768 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/onesampttestdes".
180514-11:15:01,771 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:15:01,774 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:15:01,780 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")180514-11:15:01,775 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:15:01,795 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:15:03,639 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:15:31,230 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,503 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,619 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,647 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,666 workflow INFO:
[Job 15] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:31,669 workflow INFO:
[Job 20] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:31,672 workflow INFO:
[Job 25] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:31,676 workflow INFO:
[Job 35] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:31,682 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:15:31,721 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,740 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,744 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2estimate".180514-11:15:31,748 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,752 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2estimate".180514-11:15:31,755 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,754 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,758 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2estimate".
180514-11:15:31,761 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,769 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,774 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".180514-11:15:31,768 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2estimate".
180514-11:15:31,788 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,792 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:15:31,788 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:31,807 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:15:31,810 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:15:31,825 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:15:31,834 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:31,910 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:15:33,671 workflow INFO:
[Job 30] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:33,674 workflow INFO:
[Job 40] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:33,677 workflow INFO:
[Job 45] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:33,681 workflow INFO:
[Job 50] Completed (spm_l2analysis.onesampttestdes).
180514-11:15:33,686 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:15:33,740 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,746 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,744 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2estimate".180514-11:15:33,752 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,751 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2estimate".
180514-11:15:33,758 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2estimate".180514-11:15:33,760 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".180514-11:15:33,763 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,768 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2estimate".
180514-11:15:33,775 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,781 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-11:15:33,790 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:15:33,805 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".180514-11:15:33,807 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:15:33,826 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:15:33,842 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:15:35,678 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:16:10,664 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:11,93 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:11,447 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:11,519 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:11,717 workflow INFO:
[Job 16] Completed (spm_l2analysis.level2estimate).
180514-11:16:11,723 workflow INFO:
[Job 21] Completed (spm_l2analysis.level2estimate).
180514-11:16:11,729 workflow INFO:
[Job 26] Completed (spm_l2analysis.level2estimate).
180514-11:16:11,735 workflow INFO:
[Job 36] Completed (spm_l2analysis.level2estimate).
180514-11:16:11,743 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:16:11,796 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:11,800 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2conestimate".
180514-11:16:11,803 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:16:11,804 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:11,810 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:11,808 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2conestimate".
180514-11:16:11,815 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2conestimate".180514-11:16:11,819 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:11,818 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:16:11,821 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:16:11,817 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:11,823 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2conestimate".
180514-11:16:11,832 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:16:11,833 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:16:11,842 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:16:11,857 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:16:12,347 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:12,395 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:12,421 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:12,861 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:16:13,718 workflow INFO:
[Job 31] Completed (spm_l2analysis.level2estimate).
180514-11:16:13,720 workflow INFO:
[Job 41] Completed (spm_l2analysis.level2estimate).
180514-11:16:13,723 workflow INFO:
[Job 46] Completed (spm_l2analysis.level2estimate).
180514-11:16:13,725 workflow INFO:
[Job 51] Completed (spm_l2analysis.level2estimate).
180514-11:16:13,730 workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:16:13,788 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,792 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2conestimate".
180514-11:16:13,797 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,796 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,809 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,802 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2conestimate".180514-11:16:13,813 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:16:13,814 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2conestimate".
180514-11:16:13,821 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,829 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:16:13,826 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2conestimate".
180514-11:16:13,839 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,844 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:16:13,863 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:16:13,866 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")180514-11:16:13,866 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:16:15,724 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:16:36,906 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:36,918 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".180514-11:16:36,919 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:36,938 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:37,342 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:37,754 workflow INFO:
[Job 17] Completed (spm_l2analysis.level2conestimate).
180514-11:16:37,759 workflow INFO:
[Job 22] Completed (spm_l2analysis.level2conestimate).
180514-11:16:37,764 workflow INFO:
[Job 27] Completed (spm_l2analysis.level2conestimate).
180514-11:16:37,766 workflow INFO:
[Job 37] Completed (spm_l2analysis.level2conestimate).
180514-11:16:37,768 workflow INFO:
[Job 52] Completed (spm_l2analysis.level2conestimate).
180514-11:16:37,771 workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:16:37,817 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,820 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/level2thresh".
180514-11:16:37,823 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,823 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,826 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/level2thresh".180514-11:16:37,832 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,835 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/level2thresh".
180514-11:16:37,839 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,839 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:16:37,845 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,839 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,841 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:16:37,843 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/level2thresh".
180514-11:16:37,849 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/level2thresh".
180514-11:16:37,854 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:16:37,856 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:16:37,856 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:37,859 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:16:37,871 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:16:37,871 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:16:38,124 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:38,169 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:38,227 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:16:39,754 workflow INFO:
[Job 32] Completed (spm_l2analysis.level2conestimate).
180514-11:16:39,757 workflow INFO:
[Job 42] Completed (spm_l2analysis.level2conestimate).
180514-11:16:39,759 workflow INFO:
[Job 47] Completed (spm_l2analysis.level2conestimate).
180514-11:16:39,764 workflow INFO:
[MultiProc] Running 5 tasks, and 9 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:16:39,824 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:39,832 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/level2thresh".180514-11:16:39,836 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:39,838 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:16:39,840 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/level2thresh".
180514-11:16:39,843 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:16:39,846 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:39,849 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/level2thresh".
180514-11:16:39,852 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:16:39,858 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:16:39,867 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")180514-11:16:39,871 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:16:41,758 workflow INFO:
[MultiProc] Running 8 tasks, and 6 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:16:50,770 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:50,865 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:50,970 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:51,550 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:51,591 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:51,768 workflow INFO:
[Job 18] Completed (spm_l2analysis.level2thresh).
180514-11:16:51,773 workflow INFO:
[Job 23] Completed (spm_l2analysis.level2thresh).
180514-11:16:51,780 workflow INFO:
[Job 28] Completed (spm_l2analysis.level2thresh).
180514-11:16:51,787 workflow INFO:
[Job 38] Completed (spm_l2analysis.level2thresh).
180514-11:16:51,794 workflow INFO:
[Job 53] Completed (spm_l2analysis.level2thresh).
180514-11:16:51,802 workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:16:51,857 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,861 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_8/datasink".
180514-11:16:51,864 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,868 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,873 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:16:51,874 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0007_fwhm_id_4/datasink".
180514-11:16:51,877 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0007_fwhm8/SPM.mat
180514-11:16:51,878 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,880 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm8/spmT_0001.nii180514-11:16:51,882 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,885 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm8/con_0001.nii
180514-11:16:51,888 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm8/spmT_0001_thr.nii180514-11:16:51,889 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:16:51,888 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_8/datasink".
180514-11:16:51,894 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:16:51,895 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0007_fwhm4/SPM.mat
180514-11:16:51,900 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,896 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:51,900 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm4/spmT_0001.nii180514-11:16:51,904 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:16:51,907 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm4/con_0001.nii180514-11:16:51,908 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_8/datasink".180514-11:16:51,908 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0006_fwhm8/SPM.mat
180514-11:16:51,911 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:16:51,912 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm8/spmT_0001.nii
180514-11:16:51,915 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm8/con_0001.nii
180514-11:16:51,919 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:51,918 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm8/spmT_0001_thr.nii
180514-11:16:51,923 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:16:51,925 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0007_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0007_fwhm4/spmT_0001_thr.nii
180514-11:16:51,925 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_4/datasink".180514-11:16:51,926 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:51,929 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0005_fwhm8/SPM.mat
180514-11:16:51,934 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001.nii
180514-11:16:51,936 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:51,938 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm8/con_0001.nii
180514-11:16:51,941 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:16:51,942 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001_thr.nii
180514-11:16:51,951 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:16:51,948 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:51,955 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0004_fwhm4/SPM.mat
180514-11:16:51,958 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm4/spmT_0001.nii
180514-11:16:51,960 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm4/con_0001.nii
180514-11:16:51,963 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm4/spmT_0001_thr.nii
180514-11:16:51,969 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:52,941 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:53,45 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:53,48 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:16:53,770 workflow INFO:
[Job 33] Completed (spm_l2analysis.level2thresh).
180514-11:16:53,775 workflow INFO:
[Job 43] Completed (spm_l2analysis.level2thresh).
180514-11:16:53,780 workflow INFO:
[Job 48] Completed (spm_l2analysis.level2thresh).
180514-11:16:53,785 workflow INFO:
[Job 19] Completed (spm_l2analysis.datasink).
180514-11:16:53,791 workflow INFO:
[Job 24] Completed (spm_l2analysis.datasink).
180514-11:16:53,796 workflow INFO:
[Job 29] Completed (spm_l2analysis.datasink).
180514-11:16:53,801 workflow INFO:
[Job 39] Completed (spm_l2analysis.datasink).
180514-11:16:53,806 workflow INFO:
[Job 54] Completed (spm_l2analysis.datasink).
180514-11:16:53,811 workflow INFO:
[MultiProc] Running 0 tasks, and 9 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-11:16:53,866 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:53,873 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0006_fwhm_id_4/datasink".
180514-11:16:53,876 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:16:53,880 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:53,884 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0005_fwhm_id_4/datasink".
180514-11:16:53,887 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:16:53,889 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:53,889 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:16:53,895 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0006_fwhm4/SPM.mat180514-11:16:53,894 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0004_fwhm_id_8/datasink".180514-11:16:53,896 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:16:53,899 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,898 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:16:53,905 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,904 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/onesampttestdes".
180514-11:16:53,909 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-11:16:53,909 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm4/spmT_0001.nii180514-11:16:53,901 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0005_fwhm4/SPM.mat180514-11:16:53,908 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".180514-11:16:53,909 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/onesampttestdes".
180514-11:16:53,914 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001.nii180514-11:16:53,915 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,916 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,918 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm4/con_0001.nii
180514-11:16:53,923 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,918 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:53,922 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/onesampttestdes".180514-11:16:53,921 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0005_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001_thr.nii
180514-11:16:53,927 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:53,929 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm4/con_0001.nii180514-11:16:53,930 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0004_fwhm8/SPM.mat
180514-11:16:53,929 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".180514-11:16:53,930 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/onesampttestdes".
180514-11:16:53,937 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,942 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0006_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0006_fwhm4/spmT_0001_thr.nii180514-11:16:53,944 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,939 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:53,935 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm8/spmT_0001.nii180514-11:16:53,945 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:53,949 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm8/con_0001.nii
180514-11:16:53,951 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:53,953 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0004_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0004_fwhm8/spmT_0001_thr.nii180514-11:16:53,954 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/onesampttestdes".
180514-11:16:53,965 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:53,965 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:53,970 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
180514-11:16:53,985 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:55,776 workflow INFO:
[Job 34] Completed (spm_l2analysis.datasink).
180514-11:16:55,779 workflow INFO:
[Job 44] Completed (spm_l2analysis.datasink).
180514-11:16:55,781 workflow INFO:
[Job 49] Completed (spm_l2analysis.datasink).
180514-11:16:55,787 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:16:55,840 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:55,845 workflow INFO:
[Node] Setting-up "spm_l2analysis.onesampttestdes" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/onesampttestdes".
180514-11:16:55,861 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.onesampttestdes".
180514-11:16:55,875 workflow INFO:
[Node] Running "onesampttestdes" ("nipype.interfaces.spm.model.OneSampleTTestDesign")
180514-11:16:57,780 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:17:11,620 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:11,658 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:11,749 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:11,792 workflow INFO:
[Job 55] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:11,793 workflow INFO:
[Job 65] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:11,796 workflow INFO:
[Job 70] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:11,801 workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
* spm_l2analysis.onesampttestdes
180514-11:17:11,845 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:11,849 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:11,849 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2estimate".
180514-11:17:11,851 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".180514-11:17:11,852 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2estimate".180514-11:17:11,855 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:11,855 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".180514-11:17:11,858 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2estimate".
180514-11:17:11,867 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:11,872 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:11,880 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:11,889 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:12,130 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:12,237 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:13,794 workflow INFO:
[Job 60] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:13,797 workflow INFO:
[Job 75] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:13,801 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.onesampttestdes
180514-11:17:13,854 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:13,862 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2estimate".180514-11:17:13,867 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:13,874 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2estimate".
180514-11:17:13,878 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:13,876 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:13,899 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:13,914 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:13,954 workflow INFO:
[Node] Finished "spm_l2analysis.onesampttestdes".
180514-11:17:15,796 workflow INFO:
[Job 80] Completed (spm_l2analysis.onesampttestdes).
180514-11:17:15,805 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:17:15,873 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:15,881 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2estimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2estimate".
180514-11:17:15,894 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2estimate".
180514-11:17:15,920 workflow INFO:
[Node] Running "level2estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-11:17:17,804 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:17:41,236 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:17:41,826 workflow INFO:
[Job 71] Completed (spm_l2analysis.level2estimate).
180514-11:17:41,829 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:17:41,892 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:41,896 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2conestimate".
180514-11:17:41,899 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:41,911 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:42,543 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:17:43,257 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:17:43,409 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:17:43,827 workflow INFO:
[Job 56] Completed (spm_l2analysis.level2estimate).
180514-11:17:43,830 workflow INFO:
[Job 66] Completed (spm_l2analysis.level2estimate).
180514-11:17:43,833 workflow INFO:
[Job 76] Completed (spm_l2analysis.level2estimate).
180514-11:17:43,836 workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2estimate
* spm_l2analysis.level2estimate
180514-11:17:43,886 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:43,889 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2conestimate".
180514-11:17:43,893 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:17:43,895 workflow INFO:
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[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2conestimate".
180514-11:17:43,903 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:43,902 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:17:43,907 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2conestimate".
180514-11:17:43,915 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:43,925 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".180514-11:17:43,933 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:43,947 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:44,905 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
180514-11:17:45,830 workflow INFO:
[Job 61] Completed (spm_l2analysis.level2estimate).
180514-11:17:45,834 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2estimate
180514-11:17:45,893 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:45,897 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2conestimate".
180514-11:17:45,905 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:45,929 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:46,772 workflow INFO:
[Node] Finished "spm_l2analysis.level2estimate".
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[Job 81] Completed (spm_l2analysis.level2estimate).
180514-11:17:47,844 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:17:47,916 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
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[Node] Setting-up "spm_l2analysis.level2conestimate" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2conestimate".
180514-11:17:47,935 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2conestimate".
180514-11:17:47,957 workflow INFO:
[Node] Running "level2conestimate" ("nipype.interfaces.spm.model.EstimateContrast")
180514-11:17:49,842 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:18:01,367 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:01,850 workflow INFO:
[Job 72] Completed (spm_l2analysis.level2conestimate).
180514-11:18:01,854 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:18:01,907 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:01,910 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/level2thresh".
180514-11:18:01,916 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:01,933 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:03,635 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:03,693 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:03,829 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:03,852 workflow INFO:
[Job 57] Completed (spm_l2analysis.level2conestimate).
180514-11:18:03,854 workflow INFO:
[Job 67] Completed (spm_l2analysis.level2conestimate).
180514-11:18:03,856 workflow INFO:
[Job 77] Completed (spm_l2analysis.level2conestimate).
180514-11:18:03,860 workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2conestimate
* spm_l2analysis.level2conestimate
180514-11:18:03,920 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:03,923 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/level2thresh".
180514-11:18:03,927 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:03,927 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:18:03,934 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:03,931 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/level2thresh".
180514-11:18:03,943 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".180514-11:18:03,947 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/level2thresh".180514-11:18:03,944 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:03,958 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:03,968 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:03,979 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:05,123 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:05,855 workflow INFO:
[Job 62] Completed (spm_l2analysis.level2conestimate).
180514-11:18:05,860 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2conestimate
180514-11:18:05,941 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:05,945 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/level2thresh".
180514-11:18:05,949 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:05,965 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:06,934 workflow INFO:
[Node] Finished "spm_l2analysis.level2conestimate".
180514-11:18:07,857 workflow INFO:
[Job 82] Completed (spm_l2analysis.level2conestimate).
180514-11:18:07,863 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:18:07,927 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:07,934 workflow INFO:
[Node] Setting-up "spm_l2analysis.level2thresh" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/level2thresh".
180514-11:18:07,964 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.level2thresh".
180514-11:18:07,987 workflow INFO:
[Node] Running "level2thresh" ("nipype.interfaces.spm.model.Threshold")
180514-11:18:09,859 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:18:13,899 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
180514-11:18:15,710 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
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[Node] Finished "spm_l2analysis.level2thresh".
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[Job 73] Completed (spm_l2analysis.level2thresh).
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[Job 58] Completed (spm_l2analysis.level2thresh).
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[Job 68] Completed (spm_l2analysis.level2thresh).
180514-11:18:15,874 workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
* spm_l2analysis.level2thresh
180514-11:18:15,954 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:18:15,959 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_8/datasink".
180514-11:18:15,964 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
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[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:18:15,973 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_8/datasink".180514-11:18:15,978 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:18:15,979 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:18:15,987 workflow INFO:
[Node] Finished "spm_l2analysis.level2thresh".
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[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:18:15,991 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0003_fwhm8/SPM.mat
180514-11:18:15,986 workflow INFO:
[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0002_fwhm_id_4/datasink".
180514-11:18:16,1 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:18:16,2 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:18:16,5 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm8/spmT_0001.nii
180514-11:18:16,5 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0002_fwhm8/SPM.mat180514-11:18:16,8 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm8/con_0001.nii
180514-11:18:16,16 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:18:16,14 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm8/spmT_0001_thr.nii180514-11:18:16,13 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm8/spmT_0001.nii180514-11:18:16,21 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0002_fwhm4/SPM.mat
180514-11:18:16,23 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm8/con_0001.nii
180514-11:18:16,28 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".180514-11:18:16,30 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm4/spmT_0001.nii
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sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm8/spmT_0001_thr.nii180514-11:18:16,34 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm4/con_0001.nii
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sub: /output/datasink/2ndLevel/_contrast_id_con_0002_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0002_fwhm4/spmT_0001_thr.nii
180514-11:18:16,41 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".180514-11:18:16,45 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
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[Node] Finished "spm_l2analysis.level2thresh".
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[Job 78] Completed (spm_l2analysis.level2thresh).
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[Job 63] Completed (spm_l2analysis.level2thresh).
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[Job 59] Completed (spm_l2analysis.datasink).
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[Job 69] Completed (spm_l2analysis.datasink).
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[Job 74] Completed (spm_l2analysis.datasink).
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[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* spm_l2analysis.level2thresh
180514-11:18:17,956 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
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[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0003_fwhm_id_4/datasink".
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[Node] Outdated cache found for "spm_l2analysis.datasink".
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[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_8/datasink".180514-11:18:17,978 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:18:17,981 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".180514-11:18:17,982 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0003_fwhm4/SPM.mat
180514-11:18:17,990 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm4/spmT_0001.nii180514-11:18:17,990 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
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sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm4/con_0001.nii
180514-11:18:17,994 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/SPM.mat -> /output/datasink/2ndLevel/ants_con_0001_fwhm8/SPM.mat
180514-11:18:17,996 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0003_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0003_fwhm4/spmT_0001_thr.nii
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sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm8/spmT_0001.nii
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sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm8/con_0001.nii
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[Node] Finished "spm_l2analysis.datasink".180514-11:18:18,8 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_8/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm8/spmT_0001_thr.nii
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[Node] Finished "spm_l2analysis.datasink".
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[Job 64] Completed (spm_l2analysis.datasink).
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[Job 79] Completed (spm_l2analysis.datasink).
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[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* spm_l2analysis.level2thresh
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[Node] Finished "spm_l2analysis.level2thresh".
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[Job 83] Completed (spm_l2analysis.level2thresh).
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[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
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[Node] Outdated cache found for "spm_l2analysis.datasink".
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[Node] Setting-up "spm_l2analysis.datasink" in "/output/workingdir/spm_l2analysis/_contrast_id_con_0001_fwhm_id_4/datasink".
180514-11:18:25,933 workflow INFO:
[Node] Outdated cache found for "spm_l2analysis.datasink".
180514-11:18:25,941 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-11:18:25,944 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/SPM.mat -> /output/datasink/2ndLevel/ants_con_0001_fwhm4/SPM.mat
180514-11:18:25,948 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/spmT_0001.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm4/spmT_0001.nii
180514-11:18:25,951 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/con_0001.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm4/con_0001.nii
180514-11:18:25,954 interface INFO:
sub: /output/datasink/2ndLevel/_contrast_id_con_0001_fwhm_id_4/spmT_0001_thr.nii -> /output/datasink/2ndLevel/ants_con_0001_fwhm4/spmT_0001_thr.nii
180514-11:18:25,962 workflow INFO:
[Node] Finished "spm_l2analysis.datasink".
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[Job 84] Completed (spm_l2analysis.datasink).
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[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 0x7f665c297e80>
Visualize results¶
Now we create a lot of outputs, but how do they look like? And also, what was the influence of different smoothing kernels and normalization?
Keep in mind, that the group analysis was only done on N=7 subjects, and that we chose a voxel-wise threshold of p<0.005. Nonetheless, we corrected for multiple comparisons with a cluster-wise FDR threshold of p<0.05.
So let's first look at the contrast average:
In [ ]:
from nilearn.plotting import plot_stat_map
%matplotlib inline
anatimg = '/data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c/1mm_T1.nii.gz'
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/ants_con_0001_fwhm4/spmT_0001_thr.nii', title='ants fwhm=4', dim=1,
bg_img=anatimg, threshold=2, vmax=8, display_mode='y', cut_coords=(-45, -30, -15, 0, 15), cmap='viridis');
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/spm_con_0001_fwhm4/spmT_0001_thr.nii', title='spm fwhm=4', dim=1,
bg_img=anatimg, threshold=2, vmax=8, display_mode='y', cut_coords=(-45, -30, -15, 0, 15), cmap='viridis');
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/ants_con_0001_fwhm8/spmT_0001_thr.nii', title='ants fwhm=8', dim=1,
bg_img=anatimg, threshold=2, vmax=8, display_mode='y', cut_coords=(-45, -30, -15, 0, 15), cmap='viridis');
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/spm_con_0001_fwhm8/spmT_0001_thr.nii', title='spm fwhm=8',
bg_img=anatimg, threshold=2, vmax=8, display_mode='y', cut_coords=(-45, -30, -15, 0, 15), cmap='viridis');
The results are more or less what you would expect: The peaks are more or less at the same places for the two normalization approaches and a wider smoothing has the effect of bigger clusters, while losing the sensitivity for smaller clusters.
Now, let's see other contrast -- Finger > others. Since we removed left-handed subjects, the activation is seen on the left part of the brain.
In [ ]:
from nilearn.plotting import plot_stat_map
anatimg = '/data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c/1mm_T1.nii.gz'
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001_thr.nii', title='ants fwhm=4', dim=1,
bg_img=anatimg, threshold=2, vmax=8, cmap='viridis', display_mode='y', cut_coords=(-45, -30, -15, 0, 15));
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001_thr.nii', title='spm fwhm=4', dim=1,
bg_img=anatimg, threshold=2, vmax=8, cmap='viridis', display_mode='y', cut_coords=(-45, -30, -15, 0, 15));
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001_thr.nii', title='ants fwhm=8', dim=1,
bg_img=anatimg, threshold=2, vmax=8, cmap='viridis', display_mode='y', cut_coords=(-45, -30, -15, 0, 15));
In [ ]:
plot_stat_map(
'/output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001_thr.nii', title='spm fwhm=8', dim=1,
bg_img=anatimg, threshold=2, vmax=8, cmap='viridis', display_mode='y', cut_coords=(-45, -30, -15, 0, 15));
Now, let's see the results using the glass brain plotting method.
In [ ]:
from nilearn.plotting import plot_glass_brain
plot_glass_brain(
'/output/datasink/2ndLevel/spm_con_0005_fwhm4/spmT_0001_thr.nii', colorbar=True,
threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='spm_fwhm4');
plot_glass_brain(
'/output/datasink/2ndLevel/ants_con_0005_fwhm4/spmT_0001_thr.nii', colorbar=True,
threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='ants_fwhm4');
plot_glass_brain(
'/output/datasink/2ndLevel/spm_con_0005_fwhm8/spmT_0001_thr.nii', colorbar=True,
threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='spm_fwhm8');
plot_glass_brain(
'/output/datasink/2ndLevel/ants_con_0005_fwhm8/spmT_0001_thr.nii', colorbar=True,
threshold=2, display_mode='lyrz', black_bg=True, vmax=10, title='ants_fwhm8');
