Hands-on 1: How to create a fMRI preprocessing workflow¶
The purpose of this section is that you set-up a complete fMRI analysis workflow yourself. So that in the end you are able to perform the analysis from A-Z, i.e. from preprocessing to group analysis. This section will cover the preprocessing part, and the section Hands-on 2: Analysis will handle the analysis part.
We will use this opportunity to show you some nice additional interfaces/nodes that might not be relevant to your usual analysis. But it's always nice to know that they exist. And hopefully, this will encourage you to investigate all other interfaces that Nipype can bring to the tip of your finger.
Preparation¶
Before we can start with anything we first need to download the data. For this hands-on, we will only use the right-handed subjects 2-4 and 7-9. This can be done very quickly with the following datalad command.
Note: This might take a while, as datalad needs to download ~200MB of data
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%%bash
datalad get -J 4 /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \
/data/ds000114/sub-0[234789]/ses-test/func/*fingerfootlips*
get(notneeded): /data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-03/ses-test/anat/sub-03_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-04/ses-test/anat/sub-04_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-08/ses-test/anat/sub-08_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-09/ses-test/anat/sub-09_ses-test_T1w.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] get(notneeded): /data/ds000114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz (file) [already present] action summary: get (notneeded: 12)
Preprocessing Workflow Structure¶
So let's get our hands dirty. First things first, it's always good to know which interfaces you want to use in your workflow and in which order you want to execute them. For the preprocessing workflow, I recommend that we use the following nodes:
1. Gunzip (Nipype)
2. Drop Dummy Scans (FSL)
3. Slice Time Correction (SPM)
4. Motion Correction (SPM)
5. Artifact Detection
6. Segmentation (SPM)
7. Coregistration (FSL)
8. Smoothing (FSL)
9. Apply Binary Mask (FSL)
10. Remove Linear Trends (Nipype)
Note: This workflow might be overkill concerning data manipulation, but it hopefully serves as a good Nipype exercise.
Imports¶
It's always best to have all relevant module imports at the beginning of your script. So let's import what we most certainly need.
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# Get the Node and Workflow object
from nipype import Node, Workflow
# Specify which SPM to use
from nipype.interfaces.matlab import MatlabCommand
MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')
Note: Ideally you would also put the imports of all the interfaces that you use here at the top. But as we will develop the workflow step by step, we can also import the relevant modules as we go.
Create Nodes and Workflow connections¶
Let's create all the nodes that we need! Make sure to specify all relevant inputs and keep in mind which ones you later on need to connect in your pipeline.
Workflow¶
We recommend to create the workflow and establish all its connections at a later place in your script. This helps to have everything nicely together. But for this hands-on example it makes sense to establish the connections between the nodes as we go.
And for this, we first need to create a workflow:
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# Create the workflow here
# Hint: use 'base_dir' to specify where to store the working directory
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preproc = Workflow(name='work_preproc', base_dir='/output/')
Gunzip¶
I've already created the Gunzip node as a template for the other nodes. Also, we've specified an in_file here so that we can directly test the nodes without worrying about the Input/Output data stream to the workflow. This will be taken care of in a later section.
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from nipype.algorithms.misc import Gunzip
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# Specify example input file
func_file = '/data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz'
# Initiate Gunzip node
gunzip_func = Node(Gunzip(in_file=func_file), name='gunzip_func')
Drop Dummy Scans¶
The functional images of this dataset were recorded with 4 dummy scans at the beginning (see the corresponding publication). But those dummy scans were not yet taken out from the functional images.
To better illustrate this, let's plot the time course of a random voxel of the just defined func_file:
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%matplotlib inline
import pylab as plt
import nibabel as nb
plt.plot(nb.load(func_file).get_fdata()[32, 32, 15, :]);
In the figure above, we see that at the very beginning there are extreme values, which hint to the fact that steady state wasn't reached yet. Therefore, we want to exclude the dummy scans from the original data. This can be achieved with FSL's ExtractROI.
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from nipype.interfaces.fsl import ExtractROI
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extract = Node(ExtractROI(t_min=4, t_size=-1, output_type='NIFTI'),
name="extract")
This ExtractROI node can now be connected to the gunzip_func node from above. To do this, we use the following command:
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preproc.connect([(gunzip_func, extract, [('out_file', 'in_file')])])
Slice Time Correction¶
Now to the next step. Let's us SPM's SliceTiming to correct for slice wise acquisition of the volumes. As a reminder, the tutorial dataset was recorded...
- with a time repetition (TR) of 2.5 seconds
- with 30 slices per volume
- in an interleaved fashion, i.e. slice order is [1, 3, 5, 7, ..., 2, 4, 6, ..., 30]
- with a time acquisition (TA) of 2.4167 seconds, i.e.
TR-(TR/num_slices)
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from nipype.interfaces.spm import SliceTiming
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slice_order = list(range(1, 31, 2)) + list(range(2, 31, 2))
print(slice_order)
[1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30]
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# Initiate SliceTiming node here
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slicetime = Node(SliceTiming(num_slices=30,
ref_slice=15,
slice_order=slice_order,
time_repetition=2.5,
time_acquisition=2.5-(2.5/30)),
name='slicetime')
Now the next step is to connect the SliceTiming node to the rest of the workflow, i.e. the ExtractROI node.
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# Connect SliceTiming node to the other nodes here
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preproc.connect([(extract, slicetime, [('roi_file', 'in_files')])])
Motion Correction¶
To correct for motion in the scanner, we will be using FSL's MCFLIRT.
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from nipype.interfaces.fsl import MCFLIRT
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# Initiate MCFLIRT node here
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mcflirt = Node(MCFLIRT(mean_vol=True,
save_plots=True),
name="mcflirt")
Connect the MCFLIRT node to the rest of the workflow.
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# Connect MCFLIRT node to the other nodes here
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preproc.connect([(slicetime, mcflirt, [('timecorrected_files', 'in_file')])])
Artifact Detection¶
We will use the really cool and useful ArtifactDetection tool from Nipype to detect motion and intensity outliers in the functional images. The interface is initiated as follows:
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from nipype.algorithms.rapidart import ArtifactDetect
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art = Node(ArtifactDetect(norm_threshold=2,
zintensity_threshold=2,
mask_type='spm_global',
parameter_source='FSL',
use_differences=[True, False],
plot_type='svg'),
name="art")
The parameters above mean the following:
norm_threshold- Threshold to use to detect motion-related outliers when composite motion is being usedzintensity_threshold- Intensity Z-threshold use to detection images that deviate from the meanmask_type- Type of mask that should be used to mask the functional data. spm_global uses an spm_global like calculation to determine the brain maskparameter_source- Source of movement parametersuse_differences- If you want to use differences between successive motion (first element) and intensity parameter (second element) estimates in order to determine outliers
And this is how you connect this node to the rest of the workflow:
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preproc.connect([(mcflirt, art, [('out_file', 'realigned_files'),
('par_file', 'realignment_parameters')])
])
Segmentation of anatomical image¶
Now let's work on the anatomical image. In particular, let's use SPM's NewSegment to create probability maps for the gray matter, white matter tissue and CSF.
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from nipype.interfaces.spm import NewSegment
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# Use the following tissue specification to get a GM and WM probability map
tpm_img ='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'
tissue1 = ((tpm_img, 1), 1, (True,False), (False, False))
tissue2 = ((tpm_img, 2), 1, (True,False), (False, False))
tissue3 = ((tpm_img, 3), 2, (True,False), (False, False))
tissue4 = ((tpm_img, 4), 3, (False,False), (False, False))
tissue5 = ((tpm_img, 5), 4, (False,False), (False, False))
tissue6 = ((tpm_img, 6), 2, (False,False), (False, False))
tissues = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6]
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# Initiate NewSegment node here
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segment = Node(NewSegment(tissues=tissues), name='segment')
We will again be using a Gunzip node to unzip the anatomical image that we then want to use as input to the segmentation node. We again also need to specify the anatomical image that we want to use in this case. As before, this will later also be handled directly by the Input/Output stream.
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# Specify example input file
anat_file = '/data/ds000114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz'
# Initiate Gunzip node
gunzip_anat = Node(Gunzip(in_file=anat_file), name='gunzip_anat')
Now we can connect the NewSegment node to the rest of the workflow.
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# Connect NewSegment node to the other nodes here
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preproc.connect([(gunzip_anat, segment, [('out_file', 'channel_files')])])
Compute Coregistration Matrix¶
As a next step, we will make sure that the functional images are coregistered to the anatomical image. For this, we will use FSL's FLIRT function. As we just created a white matter probability map, we can use this together with the a Boundary-Based Registration (BBR) cost function do optimize the image coregistration. As some helpful notes...
- use a degree of freedom of 6
- specify the cost function as
bbr - use the
schedule='/usr/share/fsl/5.0/etc/flirtsch/bbr.sch'
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from nipype.interfaces.fsl import FLIRT
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# Initiate FLIRT node here
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coreg = Node(FLIRT(dof=6,
cost='bbr',
schedule='/usr/share/fsl/5.0/etc/flirtsch/bbr.sch',
output_type='NIFTI'),
name="coreg")
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# Connect FLIRT node to the other nodes here
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preproc.connect([(gunzip_anat, coreg, [('out_file', 'reference')]),
(mcflirt, coreg, [('mean_img', 'in_file')])
])
As mentioned above, the bbr routine can use the subject-specific white matter probability map to guide the coregistration. But for this, we need to create a binary mask out of the WM probability map. This can easily be done by FSL's Threshold interface.
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from nipype.interfaces.fsl import Threshold
# Threshold - Threshold WM probability image
threshold_WM = Node(Threshold(thresh=0.5,
args='-bin',
output_type='NIFTI'),
name="threshold_WM")
Now, to select the WM probability map that the NewSegment node created, we need some helper function. Because the output field partial_volume_files form the segmentation node, will give us a list of files, i.e. [[GM_prob], [WM_prob], [], [], [], []]. Therefore, using the following function, we can select only the last element of this list.
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# Select WM segmentation file from segmentation output
def get_wm(files):
return files[1][0]
# Connecting the segmentation node with the threshold node
preproc.connect([(segment, threshold_WM, [(('native_class_images', get_wm),
'in_file')])])
Now we can just connect this Threshold node to the coregistration node from above.
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# Connect Threshold node to coregistration node above here
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preproc.connect([(threshold_WM, coreg, [('out_file', 'wm_seg')])])
Apply Coregistration Matrix to functional image¶
Now that we know the coregistration matrix to correctly overlay the functional mean image on the subject-specific anatomy, we need to apply to coregistration to the whole time series. This can be achieved with FSL's FLIRT as follows:
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# Specify the isometric voxel resolution you want after coregistration
desired_voxel_iso = 4
# Apply coregistration warp to functional images
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=desired_voxel_iso,
output_type='NIFTI'),
name="applywarp")
Important: As you can see above, we also specified a variable desired_voxel_iso. This is very important at this stage, otherwise FLIRT will transform your functional images to a resolution of the anatomical image, which will dramatically increase the file size (e.g. to 1-10GB per file). If you don't want to change the voxel resolution, use the additional parameter no_resample=True. Important, for this to work, you still need to define apply_isoxfm=desired_voxel_iso.
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# Connecting the ApplyWarp node to all the other nodes
preproc.connect([(mcflirt, applywarp, [('out_file', 'in_file')]),
(coreg, applywarp, [('out_matrix_file', 'in_matrix_file')]),
(gunzip_anat, applywarp, [('out_file', 'reference')])
])
Smoothing¶
Next step is image smoothing. The most simple way to do this is to use FSL's or SPM's Smooth function. But for learning purposes, let's use FSL's SUSAN workflow as it is implemented in Nipype. Note that this time, we are importing a workflow instead of an interface.
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from nipype.workflows.fmri.fsl.preprocess import create_susan_smooth
If you type create_susan_smooth? you can see how to specify the input variables to the susan workflow. In particular, they are...
fwhm: set this value to 4 (or whichever value you want)mask_file: will be created in a later stepin_file: will be handled while connection to other nodes in the preproc workflow
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# Initiate SUSAN workflow here
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susan = create_susan_smooth(name='susan')
susan.inputs.inputnode.fwhm = 4
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# Connect Threshold node to coregistration node above here
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preproc.connect([(applywarp, susan, [('out_file', 'inputnode.in_files')])])
Create Binary Mask¶
There are many possible approaches on how you can mask your functional images. One of them is not at all, one is with a simple brain mask and one that only considers certain kind of brain tissue, e.g. gray matter.
For the current example, we want to create a dilated gray matter mask. For this purpose we need to:
- Resample the gray matter probability map to the same resolution as the functional images
- Threshold this resampled probability map at a specific value
- Dilate this mask by some voxels to make the mask less conservative and more inclusive
The first step can be done in many ways (eg. using freesurfer's mri_convert, nibabel) but in our case, we will use FSL's FLIRT. The trick is to use the probability mask, as input file and a reference file.
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from nipype.interfaces.fsl import FLIRT
# Initiate resample node
resample = Node(FLIRT(apply_isoxfm=desired_voxel_iso,
output_type='NIFTI'),
name="resample")
The second and third step can luckily be done with just one node. We can take almost the same Threshold node as above. We just need to add another additional argument: -dilF - which applies a maximum filtering of all voxels.
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from nipype.interfaces.fsl import Threshold
# Threshold - Threshold GM probability image
mask_GM = Node(Threshold(thresh=0.5,
args='-bin -dilF',
output_type='NIFTI'),
name="mask_GM")
# Select GM segmentation file from segmentation output
def get_gm(files):
return files[0][0]
Now we can connect the resample and the gray matter mask node to the segmentation node and each other.
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preproc.connect([(segment, resample, [(('native_class_images', get_gm), 'in_file'),
(('native_class_images', get_gm), 'reference')
]),
(resample, mask_GM, [('out_file', 'in_file')])
])
This should do the trick.
Apply the binary mask¶
Now we can connect this dilated gray matter mask to the susan node, as well as actually applying this to the resulting smoothed images.
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# Connect gray matter Mask node to the susan workflow here
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preproc.connect([(mask_GM, susan, [('out_file', 'inputnode.mask_file')])])
To apply the mask to the smoothed functional images, we will use FSL's ApplyMask interface.
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from nipype.interfaces.fsl import ApplyMask
Important: The susan workflow gives out a list of files, i.e. [smoothed_func.nii] instead of just the filename directly. If we would use a normal Node for ApplyMask this would lead to the following error:
TraitError: The 'in_file' trait of an ApplyMaskInput instance must be an existing file name, but a value of ['/output/work_preproc/susan/smooth/mapflow/_smooth0/asub-07_ses-test_task-fingerfootlips_bold_mcf_flirt_smooth.nii.gz'] <class 'list'> was specified.
To prevent this we will be using a MapNode and specify the in_file as it's iterfield. Like this, the node is capable to handle a list of inputs as it will know that it has to apply itself iteratively to the list of inputs.
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from nipype import MapNode
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# Initiate ApplyMask node here
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mask_func = MapNode(ApplyMask(output_type='NIFTI'),
name="mask_func",
iterfield=["in_file"])
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# Connect smoothed susan output file to ApplyMask node here
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preproc.connect([(susan, mask_func, [('outputnode.smoothed_files', 'in_file')]),
(mask_GM, mask_func, [('out_file', 'mask_file')])
])
Remove linear trends in functional images¶
Last but not least. Let's use Nipype's TSNR module to remove linear and quadratic trends in the functionally smoothed images. For this, you only have to specify the regress_poly parameter in the node initiation.
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from nipype.algorithms.confounds import TSNR
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# Initiate TSNR node here
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detrend = Node(TSNR(regress_poly=2), name="detrend")
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# Connect the detrend node to the other nodes here
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preproc.connect([(mask_func, detrend, [('out_file', 'in_file')])])
Datainput with SelectFiles and iterables¶
This is all nice and well. But so far we still had to specify the input values for gunzip_anat and gunzip_func ourselves. How can we scale this up to multiple subjects and/or multiple functional images and make the workflow take the input directly from the BIDS dataset?
For this, we need SelectFiles and iterables! It's rather simple, specify a template and fill-up the placeholder variables.
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# Import the SelectFiles
from nipype import SelectFiles
# String template with {}-based strings
templates = {'anat': 'sub-{subject_id}/ses-{ses_id}/anat/'
'sub-{subject_id}_ses-test_T1w.nii.gz',
'func': 'sub-{subject_id}/ses-{ses_id}/func/'
'sub-{subject_id}_ses-{ses_id}_task-{task_id}_bold.nii.gz'}
# Create SelectFiles node
sf = Node(SelectFiles(templates,
base_directory='/data/ds000114',
sort_filelist=True),
name='selectfiles')
sf.inputs.ses_id='test'
sf.inputs.task_id='fingerfootlips'
Now we can specify over which subjects the workflow should iterate. To test the workflow, let's still just look at subject 2.
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subject_list = ['07']
sf.iterables = [('subject_id', subject_list)]
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# Connect SelectFiles node to the other nodes here
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preproc.connect([(sf, gunzip_anat, [('anat', 'in_file')]),
(sf, gunzip_func, [('func', 'in_file')])])
Visualize the workflow¶
Now that we're done. Let's look at the workflow that we just created.
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# Create preproc output graph
preproc.write_graph(graph2use='colored', format='png', simple_form=True)
# Visualize the graph
from IPython.display import Image
Image(filename='/output/work_preproc/graph.png', width=750)
180514-09:56:56,605 workflow INFO: Generated workflow graph: /output/work_preproc/graph.png (graph2use=colored, simple_form=True).
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Run the Workflow¶
Now we are ready to run the workflow! Be careful about the n_procs parameter if you run a workflow in 'MultiProc' mode. n_procs specifies the number of jobs/cores your computer will use to run the workflow. If this number is too high your computer will try to execute too many things at once and will most likely crash.
Note: If you're using a Docker container and FLIRT fails to run without any good reason, you might need to change memory settings in the Docker preferences (6 GB should be enough for this workflow).
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preproc.run('MultiProc', plugin_args={'n_procs': 8})
180514-09:56:56,693 workflow INFO:
Workflow work_preproc settings: ['check', 'execution', 'logging', 'monitoring']
180514-09:56:56,726 workflow INFO:
Running in parallel.
180514-09:56:56,730 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-09:56:56,803 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_07/selectfiles".
180514-09:56:56,838 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-09:56:56,860 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-09:56:58,732 workflow INFO:
[Job 0] Completed (work_preproc.selectfiles).
180514-09:56:58,735 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-09:56:58,792 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_07/gunzip_anat".
180514-09:56:58,790 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_07/gunzip_func".
180514-09:56:58,822 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-09:56:58,826 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")
180514-09:56:59,281 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-09:56:59,647 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
180514-09:57:00,733 workflow INFO:
[Job 1] Completed (work_preproc.gunzip_func).
180514-09:57:00,735 workflow INFO:
[Job 6] Completed (work_preproc.gunzip_anat).
180514-09:57:00,737 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-09:57:00,792 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_07/segment".
180514-09:57:00,802 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")
180514-09:57:00,785 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_07/extract".
180514-09:57:00,820 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_07/gunzip_func/sub-07_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_07/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-09:57:01,127 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-09:57:02,736 workflow INFO:
[Job 2] Completed (work_preproc.extract).
180514-09:57:02,739 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.segment
180514-09:57:02,798 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_07/slicetime".
180514-09:57:02,806 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")
180514-09:57:04,738 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.slicetime
* work_preproc.segment
180514-09:57:27,694 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-09:57:28,762 workflow INFO:
[Job 3] Completed (work_preproc.slicetime).
180514-09:57:28,766 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.segment
180514-09:57:28,827 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_07/mcflirt".
180514-09:57:28,837 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_07/slicetime/asub-07_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_07/mcflirt/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-09:57:30,764 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.segment
180514-09:58:41,977 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-09:58:42,833 workflow INFO:
[Job 4] Completed (work_preproc.mcflirt).
180514-09:58:42,836 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.segment
180514-09:58:42,890 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_07/art".
180514-09:58:42,897 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2666, in run_cell
self.events.trigger('post_run_cell', result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/events.py", line 88, in trigger
func(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/pylab/backend_inline.py", line 160, in configure_once
activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-09:58:44,76 workflow INFO:
[Node] Finished "work_preproc.art".
180514-09:58:44,835 workflow INFO:
[Job 5] Completed (work_preproc.art).
180514-09:58:44,838 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.segment
180514-10:00:06,119 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:00:06,913 workflow INFO:
[Job 7] Completed (work_preproc.segment).
180514-10:00:06,921 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:00:06,991 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_07/resample".
180514-10:00:06,993 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_07/threshold_WM".
180514-10:00:07,2 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_07/segment/c2sub-07_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_07/threshold_WM/c2sub-07_ses-test_T1w_thresh.nii180514-10:00:07,2 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_07/segment/c1sub-07_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_07/segment/c1sub-07_ses-test_T1w.nii -out c1sub-07_ses-test_T1w_flirt.nii -omat c1sub-07_ses-test_T1w_flirt.mat -applyisoxfm 4.000000
180514-10:00:07,538 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:00:08,913 workflow INFO:
[Job 10] Completed (work_preproc.threshold_WM).
180514-10:00:08,916 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.resample
180514-10:00:08,979 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_07/coreg".
180514-10:00:08,987 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_07/mcflirt/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_07/gunzip_anat/sub-07_ses-test_T1w.nii -out asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_07/threshold_WM/c2sub-07_ses-test_T1w_thresh.nii
180514-10:00:10,779 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:00:10,915 workflow INFO:
[Job 8] Completed (work_preproc.resample).
180514-10:00:10,917 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.coreg
180514-10:00:10,966 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_07/mask_GM".
180514-10:00:10,973 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_07/resample/c1sub-07_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_07/mask_GM/c1sub-07_ses-test_T1w_flirt_thresh.nii
180514-10:00:11,333 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:00:12,917 workflow INFO:
[Job 9] Completed (work_preproc.mask_GM).
180514-10:00:12,920 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.coreg
180514-10:01:35,185 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:01:36,995 workflow INFO:
[Job 11] Completed (work_preproc.coreg).
180514-10:01:37,3 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:37,69 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_07/applywarp".
180514-10:01:37,77 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_07/mcflirt/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_07/gunzip_anat/sub-07_ses-test_T1w.nii -out asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_07/coreg/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline
180514-10:01:38,996 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.applywarp
180514-10:01:48,221 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:01:49,7 workflow INFO:
[Job 12] Completed (work_preproc.applywarp).
180514-10:01:49,13 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:49,81 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_07/mask".
180514-10:01:49,85 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_07/median".180514-10:01:49,88 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_07/mask/mapflow/_mask0".
180514-10:01:49,94 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_07/median/mapflow/_median0".180514-10:01:49,94 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_07/applywarp/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_07/mask_GM/c1sub-07_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_07/mask/mapflow/_mask0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
180514-10:01:49,99 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_07/applywarp/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_07/mask_GM/c1sub-07_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:01:50,433 workflow INFO:
[Node] Finished "_median0".
180514-10:01:50,438 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:01:51,8 workflow INFO:
[Job 15] Completed (work_preproc.susan.median).
180514-10:01:51,11 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.susan.mask
180514-10:01:52,397 workflow INFO:
[Node] Finished "_mask0".
180514-10:01:52,402 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:01:53,11 workflow INFO:
[Job 13] Completed (work_preproc.susan.mask).
180514-10:01:53,18 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:53,86 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_07/meanfunc2".
180514-10:01:53,93 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_07/meanfunc2/mapflow/_meanfunc20".
180514-10:01:53,99 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_07/mask/mapflow/_mask0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_07/meanfunc2/mapflow/_meanfunc20/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:01:54,364 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:01:54,370 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:01:55,13 workflow INFO:
[Job 14] Completed (work_preproc.susan.meanfunc2).
180514-10:01:55,20 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:55,89 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_07/merge".
180514-10:01:55,95 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:01:55,103 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:01:57,16 workflow INFO:
[Job 16] Completed (work_preproc.susan.merge).
180514-10:01:57,23 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:57,94 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_07/multi_inputs".
180514-10:01:57,101 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")
180514-10:01:57,109 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:01:59,16 workflow INFO:
[Job 17] Completed (work_preproc.susan.multi_inputs).
180514-10:01:59,21 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:01:59,79 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_07/smooth".
180514-10:01:59,108 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_07/smooth/mapflow/_smooth0".
180514-10:01:59,115 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_07/applywarp/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 1046.2500000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_07/meanfunc2/mapflow/_meanfunc20/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 1046.2500000000 /output/work_preproc/susan/_subject_id_07/smooth/mapflow/_smooth0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:02:01,18 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.susan.smooth
180514-10:02:38,356 workflow INFO:
[Node] Finished "_smooth0".
180514-10:02:38,362 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:02:39,55 workflow INFO:
[Job 18] Completed (work_preproc.susan.smooth).
180514-10:02:39,63 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:02:39,133 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_07/mask_func".
180514-10:02:39,140 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_07/mask_func/mapflow/_mask_func0".
180514-10:02:39,145 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_07/smooth/mapflow/_smooth0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_07/mask_GM/c1sub-07_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_07/mask_func/mapflow/_mask_func0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:02:40,163 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:02:40,168 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:02:41,55 workflow INFO:
[Job 19] Completed (work_preproc.mask_func).
180514-10:02:41,58 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:02:41,108 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_07/detrend".
180514-10:02:41,113 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:02:43,58 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.detrend
180514-10:02:46,341 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:02:47,63 workflow INFO:
[Job 20] Completed (work_preproc.detrend).
180514-10:02:47,69 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 0x7f026449ba58>
Inspect output¶
What did we actually do? Let's look at all the data that was created.
In [ ]:
!tree /output/work_preproc/ -I '*js|*json|*pklz|_report|*dot|*html|*txt|*.m'
/output/work_preproc/
├── graph.png
├── _subject_id_07
│  ├── applywarp
│  │  ├── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat
│  │  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii
│  ├── art
│  │  ├── mask.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz
│  │  └── plot.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.svg
│  ├── coreg
│  │  ├── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat
│  │  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii
│  ├── detrend
│  │  ├── detrend.nii.gz
│  │  ├── mean.nii.gz
│  │  ├── stdev.nii.gz
│  │  └── tsnr.nii.gz
│  ├── extract
│  │  └── sub-07_ses-test_task-fingerfootlips_bold_roi.nii
│  ├── gunzip_anat
│  │  └── sub-07_ses-test_T1w.nii
│  ├── gunzip_func
│  │  └── sub-07_ses-test_task-fingerfootlips_bold.nii
│  ├── mask_func
│  │  └── mapflow
│  │  └── _mask_func0
│  │  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
│  ├── mask_GM
│  │  └── c1sub-07_ses-test_T1w_flirt_thresh.nii
│  ├── mcflirt
│  │  ├── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz
│  │  ├── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz
│  │  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par
│  ├── resample
│  │  ├── c1sub-07_ses-test_T1w_flirt.mat
│  │  └── c1sub-07_ses-test_T1w_flirt.nii
│  ├── segment
│  │  ├── c1sub-07_ses-test_T1w.nii
│  │  ├── c2sub-07_ses-test_T1w.nii
│  │  └── c3sub-07_ses-test_T1w.nii
│  ├── selectfiles
│  ├── slicetime
│  │  └── asub-07_ses-test_task-fingerfootlips_bold_roi.nii
│  └── threshold_WM
│  └── c2sub-07_ses-test_T1w_thresh.nii
└── susan
└── _subject_id_07
├── mask
│  └── mapflow
│  └── _mask0
│  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
├── meanfunc2
│  └── mapflow
│  └── _meanfunc20
│  └── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
├── median
│  └── mapflow
│  └── _median0
├── merge
├── multi_inputs
└── smooth
└── mapflow
└── _smooth0
└── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
34 directories, 29 files
But what did we do specifically? Well, let's investigate.
Motion Correction and Artifact Detection¶
How much did the subject move in the scanner and where there any outliers in the functional images?
In [ ]:
%matplotlib inline
In [ ]:
# Plot the motion paramters
import numpy as np
import pylab as plt
par = np.loadtxt('/output/work_preproc/_subject_id_07/mcflirt/'
'asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par')
fig, axes = plt.subplots(2, 1, figsize=(15, 5))
axes[0].set_ylabel('rotation (radians)')
axes[0].plot(par[0:, :3])
axes[1].plot(par[0:, 3:])
axes[1].set_xlabel('time (TR)')
axes[1].set_ylabel('translation (mm)');
The motion parameters seems to look ok. What about the detection of artifacts?
In [ ]:
# Showing the artifact detection output
from IPython.display import SVG
SVG(filename='/output/work_preproc/_subject_id_07/art/'
'plot.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.svg')
Out[ ]:
Which volumes are problematic?
In [ ]:
outliers = np.loadtxt('/output/work_preproc/_subject_id_07/art/'
'art.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt')
list(outliers.astype('int'))
Out[ ]:
[9, 21, 95, 96, 105, 120, 141, 156, 157]
Masks and Probability maps¶
Let's see what all the masks and probability maps look like. For this, we will use nilearn's plot_anat function.
In [ ]:
from nilearn import image as nli
from nilearn.plotting import plot_stat_map
%matplotlib inline
output = '/output/work_preproc/_subject_id_07/'
First, let's look at the tissue probability maps.
In [ ]:
anat = output + 'gunzip_anat/sub-07_ses-test_T1w.nii'
In [ ]:
plot_stat_map(
output + 'segment/c1sub-07_ses-test_T1w.nii', title='GM prob. map', cmap=plt.cm.magma,
threshold=0.5, bg_img=anat, display_mode='z', cut_coords=range(-35, 15, 10), dim=-1);
In [ ]:
plot_stat_map(
output + 'segment/c2sub-07_ses-test_T1w.nii', title='WM prob. map', cmap=plt.cm.magma,
threshold=0.5, bg_img=anat, display_mode='z', cut_coords=range(-35, 15, 10), dim=-1);
In [ ]:
plot_stat_map(
output + 'segment/c3sub-07_ses-test_T1w.nii', title='CSF prob. map', cmap=plt.cm.magma,
threshold=0.5, bg_img=anat, display_mode='z', cut_coords=range(-35, 15, 10), dim=-1);
And how does the gray matter mask look like that we used on the functional images?
In [ ]:
plot_stat_map(
output + 'mask_GM/c1sub-07_ses-test_T1w_flirt_thresh.nii', title='dilated GM Mask', cmap=plt.cm.magma,
threshold=0.5, bg_img=anat, display_mode='z', cut_coords=range(-35, 15, 10), dim=-1);
Functional Image transformations¶
Let's also investigate the transformation that we applied to the functional images.
In [ ]:
%matplotlib inline
from nilearn import image as nli
from nilearn.plotting import plot_epi
output = '/output/work_preproc/_subject_id_07/'
In [ ]:
plot_epi(output + 'mcflirt/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz',
title='Motion Corrected mean image', display_mode='z', cut_coords=range(-40, 21, 15),
cmap=plt.cm.viridis);
In [ ]:
mean = nli.mean_img(output + 'applywarp/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii')
plot_epi(mean, title='Coregistred mean image', display_mode='z', cut_coords=range(-40, 21, 15),
cmap=plt.cm.viridis);
In [ ]:
mean = nli.mean_img('/output/work_preproc/susan/_subject_id_07/smooth/mapflow/_smooth0/'
'asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz')
plot_epi(mean, title='Smoothed mean image', display_mode='z', cut_coords=range(-40, 21, 15),
cmap=plt.cm.viridis);
In [ ]:
mean = nli.mean_img(output + 'mask_func/mapflow/_mask_func0/'
'asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii')
plot_epi(mean, title='Masked mean image', display_mode='z', cut_coords=range(-40, 21, 15),
cmap=plt.cm.viridis);
In [ ]:
plot_epi(output + 'detrend/mean.nii.gz', title='Detrended mean image', display_mode='z',
cut_coords=range(-40, 21, 15), cmap=plt.cm.viridis);
That's all nice and beautiful, but what did smoothing and detrending actually do to the data?
In [ ]:
%matplotlib inline
import nibabel as nb
output = '/output/work_preproc/_subject_id_07/'
# Load the relevant datasets
mc = nb.load(output + 'applywarp/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii')
smooth = nb.load('/output/work_preproc/susan/_subject_id_07/smooth/mapflow/'
'_smooth0/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz')
detrended_data = nb.load(output + 'detrend/detrend.nii.gz')
# Plot a representative voxel
x, y, z = 32, 34, 43
fig = plt.figure(figsize=(12, 4))
plt.plot(mc.get_data()[x, y, z, :])
plt.plot(smooth.get_data()[x, y, z, :])
plt.plot(detrended_data.get_data()[x, y, z, :])
plt.legend(['motion corrected', 'smoothed', 'detrended']);
Data output with DataSink¶
The results look fine, but we don't need all those temporary files. So let's use Datasink to keep only those files that we actually need for the 1st and 2nd level analysis.
In [ ]:
from nipype.interfaces.io import DataSink
# Initiate the datasink node
output_folder = 'datasink_handson'
datasink = Node(DataSink(base_directory='/output/',
container=output_folder),
name="datasink")
Now the next step is to specify all the output that we want to keep in our output folder output. Make sure to keep:
- from the artifact detection node the outlier file as well as the outlier plot
- from the motion correction node the motion parameters
- from the last node, the detrended functional image
In [ ]:
# Connect nodes to datasink here
In [ ]:
preproc.connect([(art, datasink, [('outlier_files', 'preproc.@outlier_files'),
('plot_files', 'preproc.@plot_files')]),
(mcflirt, datasink, [('par_file', 'preproc.@par')]),
(detrend, datasink, [('detrended_file', 'preproc.@func')]),
])
Run the workflow¶
After adding the datasink folder, let's run the preprocessing workflow again.
In [ ]:
preproc.run('MultiProc', plugin_args={'n_procs': 8})
180514-10:03:32,238 workflow INFO:
Workflow work_preproc settings: ['check', 'execution', 'logging', 'monitoring']
180514-10:03:32,274 workflow INFO:
Running in parallel.
180514-10:03:32,279 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:32,364 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_07/selectfiles".
180514-10:03:32,408 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:03:32,417 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:03:34,279 workflow INFO:
[Job 0] Completed (work_preproc.selectfiles).
180514-10:03:34,285 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:34,356 workflow INFO:
[Job 1] Cached (work_preproc.gunzip_func).
180514-10:03:34,361 workflow INFO:
[Job 6] Cached (work_preproc.gunzip_anat).
180514-10:03:36,354 workflow INFO:
[Job 2] Cached (work_preproc.extract).
180514-10:03:36,360 workflow INFO:
[Job 7] Cached (work_preproc.segment).
180514-10:03:38,285 workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:38,358 workflow INFO:
[Job 3] Cached (work_preproc.slicetime).
180514-10:03:38,364 workflow INFO:
[Job 8] Cached (work_preproc.resample).
180514-10:03:38,368 workflow INFO:
[Job 10] Cached (work_preproc.threshold_WM).
180514-10:03:40,288 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:40,355 workflow INFO:
[Job 4] Cached (work_preproc.mcflirt).
180514-10:03:40,361 workflow INFO:
[Job 9] Cached (work_preproc.mask_GM).
180514-10:03:42,359 workflow INFO:
[Node] Outdated cache found for "work_preproc.art".
180514-10:03:42,365 workflow INFO:
[Job 11] Cached (work_preproc.coreg).
180514-10:03:42,364 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_07/art".
180514-10:03:42,384 workflow INFO:
[Node] Outdated cache found for "work_preproc.art".
180514-10:03:42,396 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:03:43,440 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:03:44,291 workflow INFO:
[Job 5] Completed (work_preproc.art).
180514-10:03:44,299 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:44,380 workflow INFO:
[Job 12] Cached (work_preproc.applywarp).
180514-10:03:46,294 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:46,370 workflow INFO:
[Job 13] Cached (work_preproc.susan.mask).
180514-10:03:46,379 workflow INFO:
[Job 15] Cached (work_preproc.susan.median).
180514-10:03:48,296 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:03:48,369 workflow INFO:
[Job 14] Cached (work_preproc.susan.meanfunc2).
180514-10:03:50,366 workflow INFO:
[Job 16] Cached (work_preproc.susan.merge).
180514-10:03:52,363 workflow INFO:
[Job 17] Cached (work_preproc.susan.multi_inputs).
180514-10:03:54,375 workflow INFO:
[Job 18] Cached (work_preproc.susan.smooth).
180514-10:03:56,376 workflow INFO:
[Job 19] Cached (work_preproc.mask_func).
180514-10:03:58,374 workflow INFO:
[Node] Outdated cache found for "work_preproc.detrend".
180514-10:03:58,380 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_07/detrend".
180514-10:03:58,412 workflow INFO:
[Node] Outdated cache found for "work_preproc.detrend".
180514-10:03:58,422 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:04:00,304 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.detrend
180514-10:04:03,844 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:04:04,308 workflow INFO:
[Job 20] Completed (work_preproc.detrend).
180514-10:04:04,312 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:04,381 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_07/datasink".
180514-10:04:04,391 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:04:04,400 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:04:06,311 workflow INFO:
[Job 21] Completed (work_preproc.datasink).
180514-10:04:06,318 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 0x7f02327e86d8>
Let's look now at the output of this datasink folder.
In [ ]:
!tree /output/datasink_handson -I '*js|*json|*pklz|_report|*dot|*html|*txt|*.m'
/output/datasink_handson
└── preproc
└── _subject_id_07
├── asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par
├── detrend.nii.gz
└── plot.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.svg
2 directories, 3 files
Much better! But we're still not there yet. There are many unnecessary file specifiers that we can get rid off. To do so, we can use DataSink's substitutions parameter. For this, we create a list of tuples: on the left, we specify the string that we want to replace and on the right, with what we want to replace it with.
In [ ]:
## Use the following substitutions for the DataSink output
substitutions = [('asub', 'sub'),
('_ses-test_task-fingerfootlips_bold_roi_mcf', ''),
('.nii.gz.par', '.par'),
]
# To get rid of the folder '_subject_id_07' and renaming detrend
substitutions += [('_subject_id_%s/detrend' % s,
'_subject_id_%s/sub-%s_detrend' % (s, s)) for s in subject_list]
substitutions += [('_subject_id_%s/' % s, '') for s in subject_list]
datasink.inputs.substitutions = substitutions
Before we run the preprocessing workflow again, let's first delete the current output folder:
In [ ]:
# Delets the current output folder
!rm -rf /output/datasink_handson
In [ ]:
# Runs the preprocessing workflow again, this time with substitutions
preproc.run('MultiProc', plugin_args={'n_procs': 8})
180514-10:04:09,718 workflow INFO:
Workflow work_preproc settings: ['check', 'execution', 'logging', 'monitoring']
180514-10:04:09,751 workflow INFO:
Running in parallel.
180514-10:04:09,755 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:09,831 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_07/selectfiles".
180514-10:04:09,872 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:04:09,881 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:04:11,756 workflow INFO:
[Job 0] Completed (work_preproc.selectfiles).
180514-10:04:11,759 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:11,813 workflow INFO:
[Job 1] Cached (work_preproc.gunzip_func).
180514-10:04:11,818 workflow INFO:
[Job 6] Cached (work_preproc.gunzip_anat).
180514-10:04:13,811 workflow INFO:
[Job 2] Cached (work_preproc.extract).
180514-10:04:13,817 workflow INFO:
[Job 7] Cached (work_preproc.segment).
180514-10:04:15,758 workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:15,815 workflow INFO:
[Job 3] Cached (work_preproc.slicetime).
180514-10:04:15,820 workflow INFO:
[Job 8] Cached (work_preproc.resample).
180514-10:04:15,824 workflow INFO:
[Job 10] Cached (work_preproc.threshold_WM).
180514-10:04:17,761 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:17,841 workflow INFO:
[Job 4] Cached (work_preproc.mcflirt).
180514-10:04:17,846 workflow INFO:
[Job 9] Cached (work_preproc.mask_GM).
180514-10:04:19,815 workflow INFO:
[Job 5] Cached (work_preproc.art).
180514-10:04:19,821 workflow INFO:
[Job 11] Cached (work_preproc.coreg).
180514-10:04:21,764 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:21,822 workflow INFO:
[Job 12] Cached (work_preproc.applywarp).
180514-10:04:23,766 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:23,828 workflow INFO:
[Job 13] Cached (work_preproc.susan.mask).
180514-10:04:23,834 workflow INFO:
[Job 15] Cached (work_preproc.susan.median).
180514-10:04:25,766 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:25,826 workflow INFO:
[Job 14] Cached (work_preproc.susan.meanfunc2).
180514-10:04:27,821 workflow INFO:
[Job 16] Cached (work_preproc.susan.merge).
180514-10:04:29,835 workflow INFO:
[Job 17] Cached (work_preproc.susan.multi_inputs).
180514-10:04:31,827 workflow INFO:
[Job 18] Cached (work_preproc.susan.smooth).
180514-10:04:33,831 workflow INFO:
[Job 19] Cached (work_preproc.mask_func).
180514-10:04:35,827 workflow INFO:
[Job 20] Cached (work_preproc.detrend).
180514-10:04:37,841 workflow INFO:
[Node] Outdated cache found for "work_preproc.datasink".
180514-10:04:37,848 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_07/datasink".
180514-10:04:37,868 workflow INFO:
[Node] Outdated cache found for "work_preproc.datasink".
180514-10:04:37,879 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:04:37,883 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/detrend.nii.gz -> /output/datasink_handson/preproc/sub-07_detrend.nii.gz
180514-10:04:37,887 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-07.par
180514-10:04:37,889 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/art.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-07_outliers.txt
180514-10:04:37,892 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/plot.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-07.svg
180514-10:04:37,901 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:04:39,779 workflow INFO:
[Job 21] Completed (work_preproc.datasink).
180514-10:04:39,786 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 0x7f0265141780>
In [ ]:
!tree /output/datasink_handson -I '*js|*json|*pklz|_report|*dot|*html|*.m'
/output/datasink_handson
└── preproc
├── art.sub-07_outliers.txt
├── plot.sub-07.svg
├── sub-07_detrend.nii.gz
└── sub-07.par
1 directory, 4 files
Run Preprocessing workflow on 6 right-handed subjects¶
Perfect! Now let's run the whole workflow for right-handed subjects. For this, you just need to change the subject_list variable and run again the places where this variable is used (i.e. sf.iterables and in DataSink substitutions.
In [ ]:
# Update 'subject_list' and its dependencies here
In [ ]:
subject_list = ['02', '03', '04', '07', '08', '09']
sf.iterables = [('subject_id', subject_list)]
In [ ]:
# To get rid of the folder '_subject_id_02' and renaming detrend
substitutions += [('_subject_id_%s/detrend' % s,
'_subject_id_%s/sub-%s_detrend' % (s, s)) for s in subject_list]
substitutions += [('_subject_id_%s/' % s, '') for s in subject_list]
datasink.inputs.substitutions = substitutions
Now we can run the workflow again, this time for all right-handed subjects in parallel.
In [ ]:
# Runs the preprocessing workflow again, this time with substitutions
preproc.run('MultiProc', plugin_args={'n_procs': 8})
180514-10:04:42,589 workflow INFO:
Workflow work_preproc settings: ['check', 'execution', 'logging', 'monitoring']
180514-10:04:42,706 workflow INFO:
Running in parallel.
180514-10:04:42,713 workflow INFO:
[MultiProc] Running 0 tasks, and 6 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:42,802 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_04/selectfiles".180514-10:04:42,803 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_03/selectfiles".180514-10:04:42,804 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_02/selectfiles".
180514-10:04:42,812 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:04:42,812 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:04:42,812 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:04:42,822 workflow INFO:
[Node] Finished "work_preproc.selectfiles".180514-10:04:42,824 workflow INFO:
[Node] Finished "work_preproc.selectfiles".180514-10:04:42,824 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:04:42,797 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_08/selectfiles".
180514-10:04:42,800 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_07/selectfiles".180514-10:04:42,795 workflow INFO:
[Node] Setting-up "work_preproc.selectfiles" in "/output/work_preproc/_subject_id_09/selectfiles".
180514-10:04:42,836 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:04:42,840 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:04:42,840 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:04:42,848 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:04:42,850 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:04:42,854 workflow INFO:
[Node] Finished "work_preproc.selectfiles".
180514-10:04:44,716 workflow INFO:
[Job 0] Completed (work_preproc.selectfiles).
180514-10:04:44,722 workflow INFO:
[Job 22] Completed (work_preproc.selectfiles).
180514-10:04:44,728 workflow INFO:
[Job 44] Completed (work_preproc.selectfiles).
180514-10:04:44,734 workflow INFO:
[Job 66] Completed (work_preproc.selectfiles).
180514-10:04:44,737 workflow INFO:
[Job 88] Completed (work_preproc.selectfiles).
180514-10:04:44,739 workflow INFO:
[Job 110] Completed (work_preproc.selectfiles).
180514-10:04:44,743 workflow INFO:
[MultiProc] Running 0 tasks, and 12 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:44,800 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_09/gunzip_func".
180514-10:04:44,802 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_09/gunzip_anat".180514-10:04:44,804 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_08/gunzip_func".
180514-10:04:44,810 workflow INFO:
[Job 45] Cached (work_preproc.gunzip_func).
180514-10:04:44,809 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_08/gunzip_anat".180514-10:04:44,809 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")
180514-10:04:44,811 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-10:04:44,816 workflow INFO:
[Job 50] Cached (work_preproc.gunzip_anat).
180514-10:04:44,817 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")180514-10:04:44,816 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-10:04:44,824 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_04/gunzip_func".180514-10:04:44,826 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_04/gunzip_anat".
180514-10:04:44,838 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")
180514-10:04:44,853 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-10:04:45,242 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-10:04:45,275 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-10:04:45,412 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-10:04:45,680 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
180514-10:04:45,696 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
180514-10:04:45,715 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
180514-10:04:46,721 workflow INFO:
[Job 1] Completed (work_preproc.gunzip_func).
180514-10:04:46,726 workflow INFO:
[Job 6] Completed (work_preproc.gunzip_anat).
180514-10:04:46,733 workflow INFO:
[Job 23] Completed (work_preproc.gunzip_func).
180514-10:04:46,739 workflow INFO:
[Job 28] Completed (work_preproc.gunzip_anat).
180514-10:04:46,742 workflow INFO:
[Job 67] Completed (work_preproc.gunzip_func).
180514-10:04:46,744 workflow INFO:
[Job 72] Completed (work_preproc.gunzip_anat).
180514-10:04:46,748 workflow INFO:
[MultiProc] Running 0 tasks, and 12 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:04:46,802 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_09/extract".
180514-10:04:46,808 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_09/gunzip_func/sub-09_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_09/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:04:46,811 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_09/segment".180514-10:04:46,813 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_08/extract".
180514-10:04:46,821 workflow INFO:
[Job 46] Cached (work_preproc.extract).
180514-10:04:46,826 workflow INFO:
[Job 51] Cached (work_preproc.segment).
180514-10:04:46,821 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_08/gunzip_func/sub-08_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_08/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii 4 -1180514-10:04:46,820 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")180514-10:04:46,822 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_08/segment".
180514-10:04:46,832 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_04/extract".
180514-10:04:46,836 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")180514-10:04:46,845 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_04/gunzip_func/sub-04_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_04/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii 4 -1180514-10:04:46,846 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_04/segment".
180514-10:04:46,857 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")
180514-10:04:47,185 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-10:04:47,210 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-10:04:47,312 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-10:04:48,721 workflow INFO:
[Job 2] Completed (work_preproc.extract).
180514-10:04:48,723 workflow INFO:
[Job 24] Completed (work_preproc.extract).
180514-10:04:48,725 workflow INFO:
[Job 68] Completed (work_preproc.extract).
180514-10:04:48,729 workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:48,802 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_09/slicetime".
180514-10:04:48,807 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_08/slicetime".180514-10:04:48,811 workflow INFO:
[Job 47] Cached (work_preproc.slicetime).
180514-10:04:48,814 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")180514-10:04:48,819 workflow INFO:
[Job 52] Cached (work_preproc.resample).
180514-10:04:48,822 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")180514-10:04:48,825 workflow INFO:
[Job 54] Cached (work_preproc.threshold_WM).
180514-10:04:50,724 workflow INFO:
[MultiProc] Running 5 tasks, and 7 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:50,791 workflow INFO:
[Job 48] Cached (work_preproc.mcflirt).
180514-10:04:50,796 workflow INFO:
[Job 53] Cached (work_preproc.mask_GM).
180514-10:04:50,805 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_04/slicetime".
180514-10:04:50,816 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")
180514-10:04:52,727 workflow INFO:
[MultiProc] Running 6 tasks, and 6 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:52,802 workflow INFO:
[Job 49] Cached (work_preproc.art).
180514-10:04:52,812 workflow INFO:
[Job 55] Cached (work_preproc.coreg).
180514-10:04:54,728 workflow INFO:
[MultiProc] Running 6 tasks, and 5 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:54,814 workflow INFO:
[Job 56] Cached (work_preproc.applywarp).
180514-10:04:54,857 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_03/gunzip_func".
180514-10:04:54,877 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")
180514-10:04:55,924 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
180514-10:04:56,733 workflow INFO:
[Job 89] Completed (work_preproc.gunzip_func).
180514-10:04:56,737 workflow INFO:
[MultiProc] Running 6 tasks, and 6 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:56,818 workflow INFO:
[Job 57] Cached (work_preproc.susan.mask).
180514-10:04:56,830 workflow INFO:
[Job 59] Cached (work_preproc.susan.median).
180514-10:04:58,736 workflow INFO:
[MultiProc] Running 6 tasks, and 5 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:04:58,815 workflow INFO:
[Job 58] Cached (work_preproc.susan.meanfunc2).
180514-10:04:58,825 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_03/extract".
180514-10:04:58,842 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_03/gunzip_func/sub-03_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_03/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:04:59,377 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-10:05:00,739 workflow INFO:
[Job 90] Completed (work_preproc.extract).
180514-10:05:00,754 workflow INFO:
[MultiProc] Running 6 tasks, and 5 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:00,830 workflow INFO:
[Job 60] Cached (work_preproc.susan.merge).
180514-10:05:00,842 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_03/slicetime".
180514-10:05:00,868 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")
180514-10:05:02,743 workflow INFO:
[MultiProc] Running 7 tasks, and 4 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:02,831 workflow INFO:
[Job 61] Cached (work_preproc.susan.multi_inputs).
180514-10:05:04,819 workflow INFO:
[Job 62] Cached (work_preproc.susan.smooth).
180514-10:05:06,844 workflow INFO:
[Job 63] Cached (work_preproc.mask_func).
180514-10:05:08,819 workflow INFO:
[Job 64] Cached (work_preproc.detrend).
180514-10:05:10,905 workflow INFO:
[Node] Outdated cache found for "work_preproc.datasink".
180514-10:05:10,963 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_07/datasink".
180514-10:05:10,998 workflow INFO:
[Node] Outdated cache found for "work_preproc.datasink".
180514-10:05:11,30 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:05:11,57 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-07.par
180514-10:05:11,94 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/detrend.nii.gz -> /output/datasink_handson/preproc/sub-07_detrend.nii.gz
180514-10:05:11,137 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/art.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-07_outliers.txt
180514-10:05:11,170 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_07/plot.asub-07_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-07.svg
180514-10:05:11,218 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:05:12,754 workflow INFO:
[Job 65] Completed (work_preproc.datasink).
180514-10:05:12,763 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:12,906 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_03/gunzip_anat".
180514-10:05:12,941 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-10:05:13,574 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-10:05:14,759 workflow INFO:
[Job 94] Completed (work_preproc.gunzip_anat).
180514-10:05:14,767 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:14,924 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_03/segment".
180514-10:05:14,967 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")
180514-10:05:16,764 workflow INFO:
[MultiProc] Running 8 tasks, and 2 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:29,823 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-10:05:29,997 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-10:05:30,777 workflow INFO:
[Job 3] Completed (work_preproc.slicetime).
180514-10:05:30,794 workflow INFO:
[Job 25] Completed (work_preproc.slicetime).
180514-10:05:30,810 workflow INFO:
[MultiProc] Running 6 tasks, and 4 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:30,906 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_08/mcflirt".180514-10:05:30,902 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_09/mcflirt".
180514-10:05:30,931 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_09/slicetime/asub-09_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_09/mcflirt/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-10:05:30,966 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_08/slicetime/asub-08_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_08/mcflirt/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-10:05:32,783 workflow INFO:
[MultiProc] Running 8 tasks, and 2 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:33,922 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-10:05:34,782 workflow INFO:
[Job 69] Completed (work_preproc.slicetime).
180514-10:05:34,807 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:34,896 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_04/mcflirt".
180514-10:05:34,933 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_04/slicetime/asub-04_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_04/mcflirt/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-10:05:36,787 workflow INFO:
[MultiProc] Running 8 tasks, and 2 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:42,491 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-10:05:42,792 workflow INFO:
[Job 91] Completed (work_preproc.slicetime).
180514-10:05:42,799 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:05:42,928 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_03/mcflirt".
180514-10:05:42,964 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_03/slicetime/asub-03_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_03/mcflirt/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-10:05:44,798 workflow INFO:
[MultiProc] Running 8 tasks, and 2 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:36,686 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-10:07:36,909 workflow INFO:
[Job 70] Completed (work_preproc.mcflirt).
180514-10:07:36,928 workflow INFO:
[MultiProc] Running 7 tasks, and 3 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:36,924 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-10:07:37,7 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_04/art".
180514-10:07:37,28 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:07:38,364 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:07:38,913 workflow INFO:
[Job 26] Completed (work_preproc.mcflirt).
180514-10:07:38,916 workflow INFO:
[Job 71] Completed (work_preproc.art).
180514-10:07:38,921 workflow INFO:
[MultiProc] Running 6 tasks, and 3 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:38,991 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_08/art".180514-10:07:38,992 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_func" in "/output/work_preproc/_subject_id_02/gunzip_func".
180514-10:07:39,13 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")180514-10:07:39,20 workflow INFO:
[Node] Running "gunzip_func" ("nipype.algorithms.misc.Gunzip")
180514-10:07:39,897 workflow INFO:
[Node] Finished "work_preproc.gunzip_func".
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:07:40,380 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-10:07:40,412 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:07:40,917 workflow INFO:
[Job 4] Completed (work_preproc.mcflirt).
180514-10:07:40,919 workflow INFO:
[Job 27] Completed (work_preproc.art).
180514-10:07:40,922 workflow INFO:
[Job 111] Completed (work_preproc.gunzip_func).
180514-10:07:40,927 workflow INFO:
[MultiProc] Running 5 tasks, and 3 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:40,998 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_09/art".
180514-10:07:41,0 workflow INFO:
[Node] Setting-up "work_preproc.extract" in "/output/work_preproc/_subject_id_02/extract".
180514-10:07:41,5 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")180514-10:07:41,12 workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /output/work_preproc/_subject_id_02/gunzip_func/sub-02_ses-test_task-fingerfootlips_bold.nii /output/work_preproc/_subject_id_02/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
180514-10:07:41,37 workflow INFO:
[Node] Setting-up "work_preproc.gunzip_anat" in "/output/work_preproc/_subject_id_02/gunzip_anat".
180514-10:07:41,62 workflow INFO:
[Node] Running "gunzip_anat" ("nipype.algorithms.misc.Gunzip")
180514-10:07:41,499 workflow INFO:
[Node] Finished "work_preproc.extract".
180514-10:07:41,618 workflow INFO:
[Node] Finished "work_preproc.gunzip_anat".
180514-10:07:42,213 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:07:42,921 workflow INFO:
[Job 5] Completed (work_preproc.art).
180514-10:07:42,923 workflow INFO:
[Job 112] Completed (work_preproc.extract).
180514-10:07:42,925 workflow INFO:
[Job 116] Completed (work_preproc.gunzip_anat).
180514-10:07:42,930 workflow INFO:
[MultiProc] Running 5 tasks, and 2 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:43,1 workflow INFO:
[Node] Setting-up "work_preproc.slicetime" in "/output/work_preproc/_subject_id_02/slicetime".
180514-10:07:43,10 workflow INFO:
[Node] Running "slicetime" ("nipype.interfaces.spm.preprocess.SliceTiming")
180514-10:07:43,15 workflow INFO:
[Node] Setting-up "work_preproc.segment" in "/output/work_preproc/_subject_id_02/segment".
180514-10:07:43,50 workflow INFO:
[Node] Running "segment" ("nipype.interfaces.spm.preprocess.NewSegment")
180514-10:07:44,932 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:52,267 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-10:07:52,938 workflow INFO:
[Job 92] Completed (work_preproc.mcflirt).
180514-10:07:52,943 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:07:53,19 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_03/art".
180514-10:07:53,35 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
180514-10:07:54,266 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:07:54,942 workflow INFO:
[Job 93] Completed (work_preproc.art).
180514-10:07:54,948 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.segment
* work_preproc.slicetime
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:08:15,885 workflow INFO:
[Node] Finished "work_preproc.slicetime".
180514-10:08:16,960 workflow INFO:
[Job 113] Completed (work_preproc.slicetime).
180514-10:08:16,964 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:08:17,34 workflow INFO:
[Node] Setting-up "work_preproc.mcflirt" in "/output/work_preproc/_subject_id_02/mcflirt".
180514-10:08:17,48 workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/work_preproc/_subject_id_02/slicetime/asub-02_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/work_preproc/_subject_id_02/mcflirt/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -plots
180514-10:08:18,963 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:12,881 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:09:13,9 workflow INFO:
[Job 7] Completed (work_preproc.segment).
180514-10:09:13,13 workflow INFO:
[MultiProc] Running 5 tasks, and 2 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:13,84 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_09/resample".180514-10:09:13,86 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_09/threshold_WM".
180514-10:09:13,102 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_09/segment/c1sub-09_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_09/segment/c1sub-09_ses-test_T1w.nii -out c1sub-09_ses-test_T1w_flirt.nii -omat c1sub-09_ses-test_T1w_flirt.mat -applyisoxfm 4.000000180514-10:09:13,100 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_09/segment/c2sub-09_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_09/threshold_WM/c2sub-09_ses-test_T1w_thresh.nii
180514-10:09:13,850 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:09:15,10 workflow INFO:
[Job 10] Completed (work_preproc.threshold_WM).
180514-10:09:15,14 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.resample
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:15,83 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_09/coreg".
180514-10:09:15,99 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_09/mcflirt/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_09/gunzip_anat/sub-09_ses-test_T1w.nii -out asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_09/threshold_WM/c2sub-09_ses-test_T1w_thresh.nii
180514-10:09:17,16 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.coreg
* work_preproc.resample
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:18,989 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:09:19,21 workflow INFO:
[Job 8] Completed (work_preproc.resample).
180514-10:09:19,26 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:19,92 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_09/mask_GM".
180514-10:09:19,100 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_09/resample/c1sub-09_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_09/mask_GM/c1sub-09_ses-test_T1w_flirt_thresh.nii
180514-10:09:19,675 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:09:21,22 workflow INFO:
[Job 9] Completed (work_preproc.mask_GM).
180514-10:09:21,26 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:32,388 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:09:33,34 workflow INFO:
[Job 29] Completed (work_preproc.segment).
180514-10:09:33,38 workflow INFO:
[MultiProc] Running 5 tasks, and 2 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:33,110 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_08/resample".180514-10:09:33,112 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_08/threshold_WM".
180514-10:09:33,119 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_08/segment/c1sub-08_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_08/segment/c1sub-08_ses-test_T1w.nii -out c1sub-08_ses-test_T1w_flirt.nii -omat c1sub-08_ses-test_T1w_flirt.mat -applyisoxfm 4.000000
180514-10:09:33,122 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_08/segment/c2sub-08_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_08/threshold_WM/c2sub-08_ses-test_T1w_thresh.nii
180514-10:09:33,639 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:09:35,42 workflow INFO:
[Job 32] Completed (work_preproc.threshold_WM).
180514-10:09:35,50 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.resample
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
* work_preproc.segment
180514-10:09:35,150 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_08/coreg".
180514-10:09:35,174 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_08/mcflirt/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_08/gunzip_anat/sub-08_ses-test_T1w.nii -out asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_08/threshold_WM/c2sub-08_ses-test_T1w_thresh.nii
180514-10:09:35,272 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:09:36,969 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:09:37,41 workflow INFO:
[Job 95] Completed (work_preproc.segment).
180514-10:09:37,43 workflow INFO:
[Job 30] Completed (work_preproc.resample).
180514-10:09:37,46 workflow INFO:
[MultiProc] Running 5 tasks, and 3 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
180514-10:09:37,122 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_08/mask_GM".180514-10:09:37,126 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_03/resample".180514-10:09:37,128 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_03/threshold_WM".
180514-10:09:37,138 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_03/segment/c2sub-03_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_03/threshold_WM/c2sub-03_ses-test_T1w_thresh.nii
180514-10:09:37,148 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_03/segment/c1sub-03_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_03/segment/c1sub-03_ses-test_T1w.nii -out c1sub-03_ses-test_T1w_flirt.nii -omat c1sub-03_ses-test_T1w_flirt.mat -applyisoxfm 4.000000180514-10:09:37,154 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_08/resample/c1sub-08_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_08/mask_GM/c1sub-08_ses-test_T1w_flirt_thresh.nii
180514-10:09:37,780 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:09:37,906 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:09:39,43 workflow INFO:
[Job 31] Completed (work_preproc.mask_GM).
180514-10:09:39,67 workflow INFO:
[Job 98] Completed (work_preproc.threshold_WM).
180514-10:09:39,74 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
180514-10:09:39,155 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_03/coreg".
180514-10:09:39,163 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_03/mcflirt/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_03/gunzip_anat/sub-03_ses-test_T1w.nii -out asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_03/threshold_WM/c2sub-03_ses-test_T1w_thresh.nii
180514-10:09:41,45 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.coreg
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
* work_preproc.segment
180514-10:09:42,745 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:09:43,46 workflow INFO:
[Job 73] Completed (work_preproc.segment).
180514-10:09:43,50 workflow INFO:
[MultiProc] Running 6 tasks, and 2 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
180514-10:09:43,119 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_04/threshold_WM".180514-10:09:43,115 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_04/resample".
180514-10:09:43,134 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:09:43,147 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_04/segment/c1sub-04_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_04/segment/c1sub-04_ses-test_T1w.nii -out c1sub-04_ses-test_T1w_flirt.nii -omat c1sub-04_ses-test_T1w_flirt.mat -applyisoxfm 4.000000180514-10:09:43,139 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_04/segment/c2sub-04_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_04/threshold_WM/c2sub-04_ses-test_T1w_thresh.nii
180514-10:09:43,847 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:09:45,50 workflow INFO:
[Job 96] Completed (work_preproc.resample).
180514-10:09:45,52 workflow INFO:
[Job 76] Completed (work_preproc.threshold_WM).
180514-10:09:45,56 workflow INFO:
[MultiProc] Running 6 tasks, and 2 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
180514-10:09:45,123 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_04/coreg".
180514-10:09:45,126 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_03/mask_GM".180514-10:09:45,148 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_04/mcflirt/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_04/gunzip_anat/sub-04_ses-test_T1w.nii -out asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_04/threshold_WM/c2sub-04_ses-test_T1w_thresh.nii
180514-10:09:45,164 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_03/resample/c1sub-03_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_03/mask_GM/c1sub-03_ses-test_T1w_flirt_thresh.nii
180514-10:09:45,748 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:09:47,53 workflow INFO:
[Job 97] Completed (work_preproc.mask_GM).
180514-10:09:47,59 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.coreg
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
180514-10:09:48,144 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:09:49,54 workflow INFO:
[Job 74] Completed (work_preproc.resample).
180514-10:09:49,58 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
180514-10:09:49,127 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_04/mask_GM".
180514-10:09:49,144 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_04/resample/c1sub-04_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_04/mask_GM/c1sub-04_ses-test_T1w_flirt_thresh.nii
180514-10:09:49,771 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:09:51,54 workflow INFO:
[Job 75] Completed (work_preproc.mask_GM).
180514-10:09:51,58 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.mcflirt
* work_preproc.segment
180514-10:09:55,225 workflow INFO:
[Node] Finished "work_preproc.mcflirt".
180514-10:09:57,61 workflow INFO:
[Job 114] Completed (work_preproc.mcflirt).
180514-10:09:57,64 workflow INFO:
[MultiProc] Running 5 tasks, and 1 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.segment
180514-10:09:57,128 workflow INFO:
[Node] Setting-up "work_preproc.art" in "/output/work_preproc/_subject_id_02/art".
180514-10:09:57,136 workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:542: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/rapidart.py:398: UserWarning:
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/envs/neuro/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelapp.py", line 486, in start
self.io_loop.start()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 127, in start
self.asyncio_loop.run_forever()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 422, in run_forever
self._run_once()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/base_events.py", line 1432, in _run_once
handle._run()
File "/opt/conda/envs/neuro/lib/python3.6/asyncio/events.py", line 145, in _run
self._callback(*self._args)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/ioloop.py", line 759, in _run_callback
ret = callback()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 536, in <lambda>
self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/tornado/stack_context.py", line 276, in null_wrapper
return fn(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell
handler(stream, idents, msg)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 208, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 537, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2662, in run_cell
raw_cell, store_history, silent, shell_futures)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2785, in _run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2903, in run_ast_nodes
if self.run_code(code, result):
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-87-f5f275df5bdf>", line 1, in <module>
get_ipython().run_line_magic('matplotlib', 'inline')
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2131, in run_line_magic
result = fn(*args,**kwargs)
File "<decorator-gen-107>", line 2, in matplotlib
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magic.py", line 187, in <lambda>
call = lambda f, *a, **k: f(*a, **k)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/magics/pylab.py", line 99, in matplotlib
gui, backend = self.shell.enable_matplotlib(args.gui)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3051, in enable_matplotlib
pt.activate_matplotlib(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/IPython/core/pylabtools.py", line 311, in activate_matplotlib
matplotlib.pyplot.switch_backend(backend)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/pyplot.py", line 231, in switch_backend
matplotlib.use(newbackend, warn=False, force=True)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/__init__.py", line 1410, in use
reload(sys.modules['matplotlib.backends'])
File "/opt/conda/envs/neuro/lib/python3.6/importlib/__init__.py", line 166, in reload
_bootstrap._exec(spec, module)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/matplotlib/backends/__init__.py", line 16, in <module>
line for line in traceback.format_stack()
matplotlib.use(config.get("execution", "matplotlib_backend"))
180514-10:09:58,396 workflow INFO:
[Node] Finished "work_preproc.art".
180514-10:09:59,62 workflow INFO:
[Job 115] Completed (work_preproc.art).
180514-10:09:59,66 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.segment
180514-10:11:00,385 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:11:01,116 workflow INFO:
[Job 11] Completed (work_preproc.coreg).
180514-10:11:01,120 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.segment
180514-10:11:01,184 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_09/applywarp".
180514-10:11:01,194 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_09/mcflirt/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_09/gunzip_anat/sub-09_ses-test_T1w.nii -out asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_09/coreg/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline
180514-10:11:03,120 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.segment
180514-10:11:16,668 workflow INFO:
[Node] Finished "work_preproc.segment".
180514-10:11:17,132 workflow INFO:
[Job 117] Completed (work_preproc.segment).
180514-10:11:17,136 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:17,163 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:11:17,209 workflow INFO:
[Node] Setting-up "work_preproc.resample" in "/output/work_preproc/_subject_id_02/resample".
180514-10:11:17,211 workflow INFO:
[Node] Setting-up "work_preproc.threshold_WM" in "/output/work_preproc/_subject_id_02/threshold_WM".
180514-10:11:17,217 workflow INFO:
[Node] Running "resample" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_02/segment/c1sub-02_ses-test_T1w.nii -ref /output/work_preproc/_subject_id_02/segment/c1sub-02_ses-test_T1w.nii -out c1sub-02_ses-test_T1w_flirt.nii -omat c1sub-02_ses-test_T1w_flirt.mat -applyisoxfm 4.000000
180514-10:11:17,221 workflow INFO:
[Node] Running "threshold_WM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_02/segment/c2sub-02_ses-test_T1w.nii -thr 0.5000000000 -bin /output/work_preproc/_subject_id_02/threshold_WM/c2sub-02_ses-test_T1w_thresh.nii
180514-10:11:17,732 workflow INFO:
[Node] Finished "work_preproc.threshold_WM".
180514-10:11:19,134 workflow INFO:
[Job 12] Completed (work_preproc.applywarp).
180514-10:11:19,136 workflow INFO:
[Job 120] Completed (work_preproc.threshold_WM).
180514-10:11:19,140 workflow INFO:
[MultiProc] Running 4 tasks, and 3 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:19,209 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_09/mask".
180514-10:11:19,215 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_09/median".180514-10:11:19,217 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_09/mask/mapflow/_mask0".
180514-10:11:19,226 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_09/median/mapflow/_median0".180514-10:11:19,225 workflow INFO:
[Node] Setting-up "work_preproc.coreg" in "/output/work_preproc/_subject_id_02/coreg".
180514-10:11:19,235 workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_02/mcflirt/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg.nii.gz -ref /output/work_preproc/_subject_id_02/gunzip_anat/sub-02_ses-test_T1w.nii -out asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.nii -omat asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -cost bbr -dof 6 -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/work_preproc/_subject_id_02/threshold_WM/c2sub-02_ses-test_T1w_thresh.nii180514-10:11:19,238 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_09/applywarp/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_09/mask_GM/c1sub-09_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_09/mask/mapflow/_mask0/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
180514-10:11:19,244 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_09/applywarp/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_09/mask_GM/c1sub-09_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:11:20,501 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:11:21,138 workflow INFO:
[Job 33] Completed (work_preproc.coreg).
180514-10:11:21,142 workflow INFO:
[MultiProc] Running 6 tasks, and 1 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.coreg
* work_preproc.susan.median
* work_preproc.susan.mask
* work_preproc.resample
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:21,145 workflow INFO:
[Node] Finished "_median0".
180514-10:11:21,153 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:11:21,206 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_08/applywarp".
180514-10:11:21,218 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_08/mcflirt/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_08/gunzip_anat/sub-08_ses-test_T1w.nii -out asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_08/coreg/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline
180514-10:11:22,24 workflow INFO:
[Node] Finished "work_preproc.resample".
180514-10:11:22,278 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:11:23,141 workflow INFO:
[Job 99] Completed (work_preproc.coreg).
180514-10:11:23,143 workflow INFO:
[Job 118] Completed (work_preproc.resample).
180514-10:11:23,145 workflow INFO:
[Job 15] Completed (work_preproc.susan.median).
180514-10:11:23,150 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.susan.mask
* work_preproc.coreg
180514-10:11:23,215 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_03/applywarp".180514-10:11:23,217 workflow INFO:
[Node] Setting-up "work_preproc.mask_GM" in "/output/work_preproc/_subject_id_02/mask_GM".
180514-10:11:23,224 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_03/mcflirt/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_03/gunzip_anat/sub-03_ses-test_T1w.nii -out asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_03/coreg/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline
180514-10:11:23,227 workflow INFO:
[Node] Running "mask_GM" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_02/resample/c1sub-02_ses-test_T1w_flirt.nii -thr 0.5000000000 -bin -dilF /output/work_preproc/_subject_id_02/mask_GM/c1sub-02_ses-test_T1w_flirt_thresh.nii
180514-10:11:23,449 workflow INFO:
[Node] Finished "_mask0".
180514-10:11:23,454 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:11:23,798 workflow INFO:
[Node] Finished "work_preproc.mask_GM".
180514-10:11:25,142 workflow INFO:
[Job 13] Completed (work_preproc.susan.mask).
180514-10:11:25,145 workflow INFO:
[Job 119] Completed (work_preproc.mask_GM).
180514-10:11:25,148 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:25,213 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_09/meanfunc2".
180514-10:11:25,219 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_09/meanfunc2/mapflow/_meanfunc20".
180514-10:11:25,227 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_09/mask/mapflow/_mask0/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_09/meanfunc2/mapflow/_meanfunc20/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:11:26,827 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:11:26,833 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:11:27,145 workflow INFO:
[Job 14] Completed (work_preproc.susan.meanfunc2).
180514-10:11:27,148 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:27,208 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_09/merge".
180514-10:11:27,215 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:11:27,225 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:11:29,147 workflow INFO:
[Job 16] Completed (work_preproc.susan.merge).
180514-10:11:29,150 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:29,212 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_09/multi_inputs".
180514-10:11:29,218 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")
180514-10:11:29,226 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:11:31,149 workflow INFO:
[Job 17] Completed (work_preproc.susan.multi_inputs).
180514-10:11:31,152 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:31,225 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_09/smooth".
180514-10:11:31,235 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_09/smooth/mapflow/_smooth0".
180514-10:11:31,244 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_09/applywarp/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 1116.0000000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_09/meanfunc2/mapflow/_meanfunc20/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 1116.0000000000 /output/work_preproc/susan/_subject_id_09/smooth/mapflow/_smooth0/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:11:33,152 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.applywarp
* work_preproc.applywarp
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:34,39 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:11:34,273 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:11:35,152 workflow INFO:
[Job 34] Completed (work_preproc.applywarp).
180514-10:11:35,154 workflow INFO:
[Job 100] Completed (work_preproc.applywarp).
180514-10:11:35,158 workflow INFO:
[MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:35,225 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_08/mask".
180514-10:11:35,232 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_08/median".180514-10:11:35,231 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_08/mask/mapflow/_mask0".
180514-10:11:35,240 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_08/median/mapflow/_median0".180514-10:11:35,239 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_03/mask".180514-10:11:35,244 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_03/median".
180514-10:11:35,250 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_03/mask/mapflow/_mask0".
180514-10:11:35,255 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_03/applywarp/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_03/mask_GM/c1sub-03_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_03/mask/mapflow/_mask0/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz180514-10:11:35,243 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_08/applywarp/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_08/mask_GM/c1sub-08_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_08/mask/mapflow/_mask0/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
180514-10:11:35,252 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_08/applywarp/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_08/mask_GM/c1sub-08_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:11:35,264 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_03/median/mapflow/_median0".
180514-10:11:35,282 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_03/applywarp/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_03/mask_GM/c1sub-03_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:11:37,155 workflow INFO:
[MultiProc] Running 7 tasks, and 0 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
Currently running:
* work_preproc.susan.median
* work_preproc.susan.mask
* work_preproc.susan.median
* work_preproc.susan.mask
* work_preproc.susan.smooth
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:37,208 workflow INFO:
[Node] Finished "_median0".
180514-10:11:37,217 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:11:37,500 workflow INFO:
[Node] Finished "_median0".
180514-10:11:37,505 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:11:38,946 workflow INFO:
[Node] Finished "_mask0".
180514-10:11:38,951 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:11:39,156 workflow INFO:
[Job 35] Completed (work_preproc.susan.mask).
180514-10:11:39,158 workflow INFO:
[Job 37] Completed (work_preproc.susan.median).
180514-10:11:39,160 workflow INFO:
[Job 103] Completed (work_preproc.susan.median).
180514-10:11:39,164 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.mask
* work_preproc.susan.smooth
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:39,228 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_08/meanfunc2".
180514-10:11:39,236 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_08/meanfunc2/mapflow/_meanfunc20".
180514-10:11:39,246 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_08/mask/mapflow/_mask0/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_08/meanfunc2/mapflow/_meanfunc20/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:11:39,706 workflow INFO:
[Node] Finished "_mask0".
180514-10:11:39,712 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:11:40,522 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:11:40,527 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:11:41,158 workflow INFO:
[Job 101] Completed (work_preproc.susan.mask).
180514-10:11:41,161 workflow INFO:
[Job 36] Completed (work_preproc.susan.meanfunc2).
180514-10:11:41,165 workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:41,234 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_08/merge".
180514-10:11:41,239 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:11:41,240 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_03/meanfunc2".
180514-10:11:41,246 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:11:41,253 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_03/meanfunc2/mapflow/_meanfunc20".
180514-10:11:41,260 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_03/mask/mapflow/_mask0/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_03/meanfunc2/mapflow/_meanfunc20/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:11:42,483 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:11:42,488 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:11:43,159 workflow INFO:
[Job 38] Completed (work_preproc.susan.merge).
180514-10:11:43,161 workflow INFO:
[Job 102] Completed (work_preproc.susan.meanfunc2).
180514-10:11:43,164 workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
* work_preproc.coreg
180514-10:11:43,222 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_08/multi_inputs".
180514-10:11:43,225 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_03/merge".
180514-10:11:43,229 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")180514-10:11:43,232 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:11:43,242 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:11:43,250 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:11:43,374 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:11:45,162 workflow INFO:
[Job 77] Completed (work_preproc.coreg).
180514-10:11:45,165 workflow INFO:
[Job 39] Completed (work_preproc.susan.multi_inputs).
180514-10:11:45,167 workflow INFO:
[Job 104] Completed (work_preproc.susan.merge).
180514-10:11:45,172 workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:11:45,257 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_08/smooth".
180514-10:11:45,263 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_04/applywarp".
180514-10:11:45,266 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_03/multi_inputs".180514-10:11:45,265 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_08/smooth/mapflow/_smooth0".
180514-10:11:45,272 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_04/mcflirt/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_04/gunzip_anat/sub-04_ses-test_T1w.nii -out asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_04/coreg/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline180514-10:11:45,276 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_08/applywarp/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 1039.5000000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_08/meanfunc2/mapflow/_meanfunc20/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 1039.5000000000 /output/work_preproc/susan/_subject_id_08/smooth/mapflow/_smooth0/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:11:45,288 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")
180514-10:11:45,301 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:11:47,164 workflow INFO:
[Job 105] Completed (work_preproc.susan.multi_inputs).
180514-10:11:47,167 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.applywarp
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:11:47,235 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_03/smooth".
180514-10:11:47,242 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_03/smooth/mapflow/_smooth0".
180514-10:11:47,253 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_03/applywarp/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 981.7500000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_03/meanfunc2/mapflow/_meanfunc20/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 981.7500000000 /output/work_preproc/susan/_subject_id_03/smooth/mapflow/_smooth0/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:11:49,167 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.applywarp
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:00,15 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:12:01,174 workflow INFO:
[Job 78] Completed (work_preproc.applywarp).
180514-10:12:01,178 workflow INFO:
[MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:01,246 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_04/mask".
180514-10:12:01,255 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_04/mask/mapflow/_mask0".180514-10:12:01,255 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_04/median".
180514-10:12:01,266 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_04/applywarp/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_04/mask_GM/c1sub-04_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_04/mask/mapflow/_mask0/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
180514-10:12:01,268 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_04/median/mapflow/_median0".
180514-10:12:01,292 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_04/applywarp/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_04/mask_GM/c1sub-04_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:12:03,178 workflow INFO:
[MultiProc] Running 6 tasks, and 0 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
Currently running:
* work_preproc.susan.median
* work_preproc.susan.mask
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:03,263 workflow INFO:
[Node] Finished "_median0".
180514-10:12:03,269 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:12:05,179 workflow INFO:
[Job 81] Completed (work_preproc.susan.median).
180514-10:12:05,184 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.susan.mask
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:05,510 workflow INFO:
[Node] Finished "_mask0".
180514-10:12:05,516 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:12:07,180 workflow INFO:
[Job 79] Completed (work_preproc.susan.mask).
180514-10:12:07,185 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:07,251 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_04/meanfunc2".
180514-10:12:07,260 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_04/meanfunc2/mapflow/_meanfunc20".
180514-10:12:07,266 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_04/mask/mapflow/_mask0/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_04/meanfunc2/mapflow/_meanfunc20/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:12:08,893 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:12:08,900 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:12:09,182 workflow INFO:
[Job 80] Completed (work_preproc.susan.meanfunc2).
180514-10:12:09,187 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:09,249 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_04/merge".
180514-10:12:09,259 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:12:09,267 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:12:11,183 workflow INFO:
[Job 82] Completed (work_preproc.susan.merge).
180514-10:12:11,187 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:11,253 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_04/multi_inputs".
180514-10:12:11,263 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")
180514-10:12:11,276 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:12:13,186 workflow INFO:
[Job 83] Completed (work_preproc.susan.multi_inputs).
180514-10:12:13,190 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:13,260 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_04/smooth".
180514-10:12:13,271 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_04/smooth/mapflow/_smooth0".
180514-10:12:13,282 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_04/applywarp/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 1022.2500000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_04/meanfunc2/mapflow/_meanfunc20/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 1022.2500000000 /output/work_preproc/susan/_subject_id_04/smooth/mapflow/_smooth0/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:12:14,363 workflow INFO:
[Node] Finished "_smooth0".
180514-10:12:14,372 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:12:15,190 workflow INFO:
[Job 18] Completed (work_preproc.susan.smooth).
180514-10:12:15,194 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:15,261 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_09/mask_func".
180514-10:12:15,272 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_09/mask_func/mapflow/_mask_func0".
180514-10:12:15,281 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_09/smooth/mapflow/_smooth0/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_09/mask_GM/c1sub-09_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_09/mask_func/mapflow/_mask_func0/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:12:16,384 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:12:16,389 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:12:17,193 workflow INFO:
[Job 19] Completed (work_preproc.mask_func).
180514-10:12:17,198 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:17,288 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_09/detrend".
180514-10:12:17,294 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:12:19,198 workflow INFO:
[MultiProc] Running 5 tasks, and 0 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
Currently running:
* work_preproc.detrend
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:23,178 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:12:23,199 workflow INFO:
[Job 20] Completed (work_preproc.detrend).
180514-10:12:23,203 workflow INFO:
[MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:23,273 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_09/datasink".
180514-10:12:23,284 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:12:23,294 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_09/asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-09.par
180514-10:12:23,297 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_09/detrend.nii.gz -> /output/datasink_handson/preproc/sub-09_detrend.nii.gz
180514-10:12:23,309 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_09/art.asub-09_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-09_outliers.txt
180514-10:12:23,315 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_09/plot.asub-09_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-09.svg
180514-10:12:23,327 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:12:25,201 workflow INFO:
[Job 21] Completed (work_preproc.datasink).
180514-10:12:25,204 workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:29,210 workflow INFO:
[Node] Finished "_smooth0".
180514-10:12:29,214 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:12:31,207 workflow INFO:
[Job 40] Completed (work_preproc.susan.smooth).
180514-10:12:31,210 workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:31,288 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_08/mask_func".
180514-10:12:31,295 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_08/mask_func/mapflow/_mask_func0".
180514-10:12:31,304 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_08/smooth/mapflow/_smooth0/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_08/mask_GM/c1sub-08_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_08/mask_func/mapflow/_mask_func0/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:12:32,403 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:12:32,408 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:12:32,779 workflow INFO:
[Node] Finished "_smooth0".
180514-10:12:32,784 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:12:33,209 workflow INFO:
[Job 106] Completed (work_preproc.susan.smooth).
180514-10:12:33,212 workflow INFO:
[Job 41] Completed (work_preproc.mask_func).
180514-10:12:33,216 workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:33,298 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_08/detrend".
180514-10:12:33,306 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")180514-10:12:33,302 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_03/mask_func".
180514-10:12:33,316 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_03/mask_func/mapflow/_mask_func0".
180514-10:12:33,326 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_03/smooth/mapflow/_smooth0/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_03/mask_GM/c1sub-03_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_03/mask_func/mapflow/_mask_func0/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:12:35,50 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:12:35,58 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:12:35,209 workflow INFO:
[Job 107] Completed (work_preproc.mask_func).
180514-10:12:35,213 workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.detrend
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:35,265 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_03/detrend".
180514-10:12:35,270 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:12:37,213 workflow INFO:
[MultiProc] Running 4 tasks, and 0 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
Currently running:
* work_preproc.detrend
* work_preproc.detrend
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:38,958 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:12:39,213 workflow INFO:
[Job 42] Completed (work_preproc.detrend).
180514-10:12:39,216 workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
Currently running:
* work_preproc.detrend
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:39,286 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_08/datasink".
180514-10:12:39,295 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:12:39,299 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_08/asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-08.par
180514-10:12:39,305 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_08/detrend.nii.gz -> /output/datasink_handson/preproc/sub-08_detrend.nii.gz
180514-10:12:39,308 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_08/art.asub-08_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-08_outliers.txt
180514-10:12:39,313 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_08/plot.asub-08_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-08.svg
180514-10:12:39,321 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:12:40,450 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:12:41,214 workflow INFO:
[Job 108] Completed (work_preproc.detrend).
180514-10:12:41,216 workflow INFO:
[Job 43] Completed (work_preproc.datasink).
180514-10:12:41,219 workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:41,280 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_03/datasink".
180514-10:12:41,293 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:12:41,299 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_03/asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-03.par
180514-10:12:41,303 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_03/detrend.nii.gz -> /output/datasink_handson/preproc/sub-03_detrend.nii.gz
180514-10:12:41,307 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_03/art.asub-03_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-03_outliers.txt
180514-10:12:41,310 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_03/plot.asub-03_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-03.svg
180514-10:12:41,318 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:12:43,216 workflow INFO:
[Job 109] Completed (work_preproc.datasink).
180514-10:12:43,218 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.susan.smooth
* work_preproc.coreg
180514-10:12:55,76 workflow INFO:
[Node] Finished "_smooth0".
180514-10:12:55,81 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:12:55,228 workflow INFO:
[Job 84] Completed (work_preproc.susan.smooth).
180514-10:12:55,231 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.coreg
180514-10:12:55,295 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_04/mask_func".
180514-10:12:55,302 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_04/mask_func/mapflow/_mask_func0".
180514-10:12:55,308 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_04/smooth/mapflow/_smooth0/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_04/mask_GM/c1sub-04_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_04/mask_func/mapflow/_mask_func0/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:12:56,288 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:12:56,293 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:12:57,230 workflow INFO:
[Job 85] Completed (work_preproc.mask_func).
180514-10:12:57,234 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.coreg
180514-10:12:57,286 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_04/detrend".
180514-10:12:57,292 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:12:59,49 workflow INFO:
[Node] Finished "work_preproc.coreg".
180514-10:12:59,232 workflow INFO:
[Job 121] Completed (work_preproc.coreg).
180514-10:12:59,235 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.detrend
180514-10:12:59,292 workflow INFO:
[Node] Setting-up "work_preproc.applywarp" in "/output/work_preproc/_subject_id_02/applywarp".
180514-10:12:59,299 workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/work_preproc/_subject_id_02/mcflirt/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz -ref /output/work_preproc/_subject_id_02/gunzip_anat/sub-02_ses-test_T1w.nii -out asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -omat asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.mat -applyisoxfm 4.000000 -init /output/work_preproc/_subject_id_02/coreg/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz_mean_reg_flirt.mat -interp spline
180514-10:13:01,236 workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 53.54/53.94, Free processors: 6/8.
Currently running:
* work_preproc.applywarp
* work_preproc.detrend
180514-10:13:01,918 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:13:03,237 workflow INFO:
[Job 86] Completed (work_preproc.detrend).
180514-10:13:03,242 workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.applywarp
180514-10:13:03,322 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_04/datasink".
180514-10:13:03,331 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:13:03,336 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_04/asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-04.par
180514-10:13:03,339 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_04/detrend.nii.gz -> /output/datasink_handson/preproc/sub-04_detrend.nii.gz
180514-10:13:03,343 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_04/art.asub-04_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-04_outliers.txt
180514-10:13:03,345 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_04/plot.asub-04_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-04.svg
180514-10:13:03,351 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:13:05,238 workflow INFO:
[Job 87] Completed (work_preproc.datasink).
180514-10:13:05,242 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.applywarp
180514-10:13:09,424 workflow INFO:
[Node] Finished "work_preproc.applywarp".
180514-10:13:11,247 workflow INFO:
[Job 122] Completed (work_preproc.applywarp).
180514-10:13:11,256 workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:11,319 workflow INFO:
[Node] Setting-up "work_preproc.susan.mask" in "/output/work_preproc/susan/_subject_id_02/mask".
180514-10:13:11,325 workflow INFO:
[Node] Setting-up "_mask0" in "/output/work_preproc/susan/_subject_id_02/mask/mapflow/_mask0".180514-10:13:11,326 workflow INFO:
[Node] Setting-up "work_preproc.susan.median" in "/output/work_preproc/susan/_subject_id_02/median".
180514-10:13:11,332 workflow INFO:
[Node] Setting-up "_median0" in "/output/work_preproc/susan/_subject_id_02/median/mapflow/_median0".180514-10:13:11,333 workflow INFO:
[Node] Running "_mask0" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/_subject_id_02/applywarp/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -mas /output/work_preproc/_subject_id_02/mask_GM/c1sub-02_ses-test_T1w_flirt_thresh.nii /output/work_preproc/susan/_subject_id_02/mask/mapflow/_mask0/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz
180514-10:13:11,338 workflow INFO:
[Node] Running "_median0" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /output/work_preproc/_subject_id_02/applywarp/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii -k /output/work_preproc/_subject_id_02/mask_GM/c1sub-02_ses-test_T1w_flirt_thresh.nii -p 50
180514-10:13:12,579 workflow INFO:
[Node] Finished "_median0".
180514-10:13:12,585 workflow INFO:
[Node] Finished "work_preproc.susan.median".
180514-10:13:13,245 workflow INFO:
[Job 125] Completed (work_preproc.susan.median).
180514-10:13:13,249 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.susan.mask
180514-10:13:14,303 workflow INFO:
[Node] Finished "_mask0".
180514-10:13:14,308 workflow INFO:
[Node] Finished "work_preproc.susan.mask".
180514-10:13:15,250 workflow INFO:
[Job 123] Completed (work_preproc.susan.mask).
180514-10:13:15,257 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:15,314 workflow INFO:
[Node] Setting-up "work_preproc.susan.meanfunc2" in "/output/work_preproc/susan/_subject_id_02/meanfunc2".
180514-10:13:15,320 workflow INFO:
[Node] Setting-up "_meanfunc20" in "/output/work_preproc/susan/_subject_id_02/meanfunc2/mapflow/_meanfunc20".
180514-10:13:15,327 workflow INFO:
[Node] Running "_meanfunc20" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_02/mask/mapflow/_mask0/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask.nii.gz -Tmean /output/work_preproc/susan/_subject_id_02/meanfunc2/mapflow/_meanfunc20/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz
180514-10:13:16,512 workflow INFO:
[Node] Finished "_meanfunc20".
180514-10:13:16,517 workflow INFO:
[Node] Finished "work_preproc.susan.meanfunc2".
180514-10:13:17,252 workflow INFO:
[Job 124] Completed (work_preproc.susan.meanfunc2).
180514-10:13:17,259 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:17,316 workflow INFO:
[Node] Setting-up "work_preproc.susan.merge" in "/output/work_preproc/susan/_subject_id_02/merge".
180514-10:13:17,321 workflow INFO:
[Node] Running "merge" ("nipype.interfaces.utility.base.Merge")
180514-10:13:17,327 workflow INFO:
[Node] Finished "work_preproc.susan.merge".
180514-10:13:19,256 workflow INFO:
[Job 126] Completed (work_preproc.susan.merge).
180514-10:13:19,261 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:19,345 workflow INFO:
[Node] Setting-up "work_preproc.susan.multi_inputs" in "/output/work_preproc/susan/_subject_id_02/multi_inputs".
180514-10:13:19,351 workflow INFO:
[Node] Running "multi_inputs" ("nipype.interfaces.utility.wrappers.Function")
180514-10:13:19,358 workflow INFO:
[Node] Finished "work_preproc.susan.multi_inputs".
180514-10:13:21,256 workflow INFO:
[Job 127] Completed (work_preproc.susan.multi_inputs).
180514-10:13:21,266 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:21,329 workflow INFO:
[Node] Setting-up "work_preproc.susan.smooth" in "/output/work_preproc/susan/_subject_id_02/smooth".
180514-10:13:21,338 workflow INFO:
[Node] Setting-up "_smooth0" in "/output/work_preproc/susan/_subject_id_02/smooth/mapflow/_smooth0".
180514-10:13:21,345 workflow INFO:
[Node] Running "_smooth0" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /output/work_preproc/_subject_id_02/applywarp/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt.nii 1018.5000000000 1.6986436006 3 1 1 /output/work_preproc/susan/_subject_id_02/meanfunc2/mapflow/_meanfunc20/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_mask_mean.nii.gz 1018.5000000000 /output/work_preproc/susan/_subject_id_02/smooth/mapflow/_smooth0/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz
180514-10:13:23,257 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.susan.smooth
180514-10:13:55,650 workflow INFO:
[Node] Finished "_smooth0".
180514-10:13:55,655 workflow INFO:
[Node] Finished "work_preproc.susan.smooth".
180514-10:13:57,293 workflow INFO:
[Job 128] Completed (work_preproc.susan.smooth).
180514-10:13:57,300 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:57,361 workflow INFO:
[Node] Setting-up "work_preproc.mask_func" in "/output/work_preproc/_subject_id_02/mask_func".
180514-10:13:57,367 workflow INFO:
[Node] Setting-up "_mask_func0" in "/output/work_preproc/_subject_id_02/mask_func/mapflow/_mask_func0".
180514-10:13:57,373 workflow INFO:
[Node] Running "_mask_func0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /output/work_preproc/susan/_subject_id_02/smooth/mapflow/_smooth0/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth.nii.gz -mas /output/work_preproc/_subject_id_02/mask_GM/c1sub-02_ses-test_T1w_flirt_thresh.nii /output/work_preproc/_subject_id_02/mask_func/mapflow/_mask_func0/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_flirt_smooth_masked.nii
180514-10:13:58,353 workflow INFO:
[Node] Finished "_mask_func0".
180514-10:13:58,358 workflow INFO:
[Node] Finished "work_preproc.mask_func".
180514-10:13:59,297 workflow INFO:
[Job 129] Completed (work_preproc.mask_func).
180514-10:13:59,302 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:13:59,385 workflow INFO:
[Node] Setting-up "work_preproc.detrend" in "/output/work_preproc/_subject_id_02/detrend".
180514-10:13:59,390 workflow INFO:
[Node] Running "detrend" ("nipype.algorithms.confounds.TSNR")
180514-10:14:01,297 workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 53.74/53.94, Free processors: 7/8.
Currently running:
* work_preproc.detrend
180514-10:14:04,904 workflow INFO:
[Node] Finished "work_preproc.detrend".
180514-10:14:05,301 workflow INFO:
[Job 130] Completed (work_preproc.detrend).
180514-10:14:05,312 workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:14:05,374 workflow INFO:
[Node] Setting-up "work_preproc.datasink" in "/output/work_preproc/_subject_id_02/datasink".
180514-10:14:05,384 workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:14:05,388 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_02/asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.gz.par -> /output/datasink_handson/preproc/sub-02.par
180514-10:14:05,391 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_02/detrend.nii.gz -> /output/datasink_handson/preproc/sub-02_detrend.nii.gz
180514-10:14:05,394 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_02/art.asub-02_ses-test_task-fingerfootlips_bold_roi_mcf_outliers.txt -> /output/datasink_handson/preproc/art.sub-02_outliers.txt
180514-10:14:05,396 interface INFO:
sub: /output/datasink_handson/preproc/_subject_id_02/plot.asub-02_ses-test_task-fingerfootlips_bold_roi_mcf.svg -> /output/datasink_handson/preproc/plot.sub-02.svg
180514-10:14:05,402 workflow INFO:
[Node] Finished "work_preproc.datasink".
180514-10:14:07,304 workflow INFO:
[Job 131] Completed (work_preproc.datasink).
180514-10:14:07,312 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 0x7f0265141b38>
Now we're ready for the next section Hands-on 2: How to create a fMRI analysis workflow!