Example 1: Preprocessing Workflow¶
This is meant as a very simple example for a preprocessing workflow. In this workflow we will conduct the following steps:
Motion correction of functional images with FSL’s MCFLIRT
Coregistration of functional images to anatomical images (according to FSL’s FEAT pipeline)
Smoothing of coregistered functional images with FWHM set to 4mm and 8mm
Artifact Detection in functional images (to detect outlier volumes)
Preparation¶
Before we can start with anything we first need to download the data (the other 9 subjects in the dataset). This can be done very quickly with the following datalad command.
Note: This might take a while, as datalad needs to download ~700MB of data
%%bash
datalad get -J 4 -d /home/neuro/workshop/data/ds000114 \
/home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \
/home/neuro/workshop/data/ds000114/sub-*/ses-test/func/*fingerfootlips*
action summary:
get (notneeded: 31)
It is highly recommended to configure Git before using DataLad. Set both 'user.name' and 'user.email' configuration variables.
It is highly recommended to configure Git before using DataLad. Set both 'user.name' and 'user.email' configuration variables.
Inspect the data¶
For every subject we have one anatomical T1w and 5 functional images. As a short recap, the image properties of the anatomy and the fingerfootlips functional image are:
%%bash
cd /home/neuro/workshop/data/ds000114/
nib-ls derivatives/fmriprep/sub-01/anat/*t1w_preproc.nii.gz sub-01/ses-test/f*/*fingerfootlips*.nii.gz
derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz float32 [256, 156, 256] 1.00x1.30x1.00 sform
sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz int16 [ 64, 64, 30, 184] 4.00x4.00x4.00x2.50 sform
So, let’s start!
Imports¶
First, let’s import all the modules we later will be needing.
from nilearn import plotting
%matplotlib inline
from os.path import join as opj
import os
import json
from nipype.interfaces.fsl import (BET, ExtractROI, FAST, FLIRT, ImageMaths,
MCFLIRT, SliceTimer, Threshold)
from nipype.interfaces.spm import Smooth
from nipype.interfaces.utility import IdentityInterface
from nipype.interfaces.io import SelectFiles, DataSink
from nipype.algorithms.rapidart import ArtifactDetect
from nipype import Workflow, Node
Experiment parameters¶
It’s always a good idea to specify all parameters that might change between experiments at the beginning of your script. We will use one functional image for fingerfootlips task for ten subjects.
experiment_dir = '/output'
output_dir = 'datasink'
working_dir = 'workingdir'
# list of subject identifiers
subject_list = ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']
# list of session identifiers
task_list = ['fingerfootlips']
# Smoothing widths to apply
fwhm = [4, 8]
# TR of functional images
with open('/home/neuro/workshop/data/ds000114/task-fingerfootlips_bold.json', 'rt') as fp:
task_info = json.load(fp)
TR = task_info['RepetitionTime']
# Isometric resample of functional images to voxel size (in mm)
iso_size = 4
Specify Nodes for the main workflow¶
Initiate all the different interfaces (represented as nodes) that you want to use in your workflow.
# ExtractROI - skip dummy scans
extract = Node(ExtractROI(t_min=4, t_size=-1, output_type='NIFTI'),
name="extract")
# MCFLIRT - motion correction
mcflirt = Node(MCFLIRT(mean_vol=True,
save_plots=True,
output_type='NIFTI'),
name="mcflirt")
# SliceTimer - correct for slice wise acquisition
slicetimer = Node(SliceTimer(index_dir=False,
interleaved=True,
output_type='NIFTI',
time_repetition=TR),
name="slicetimer")
# Smooth - image smoothing
smooth = Node(Smooth(), name="smooth")
smooth.iterables = ("fwhm", fwhm)
# Artifact Detection - determines outliers in functional images
art = Node(ArtifactDetect(norm_threshold=2,
zintensity_threshold=3,
mask_type='spm_global',
parameter_source='FSL',
use_differences=[True, False],
plot_type='svg'),
name="art")
Coregistration Workflow¶
Initiate a workflow that coregistrates the functional images to the anatomical image (according to FSL’s FEAT pipeline).
# BET - Skullstrip anatomical Image
bet_anat = Node(BET(frac=0.5,
robust=True,
output_type='NIFTI_GZ'),
name="bet_anat")
# FAST - Image Segmentation
segmentation = Node(FAST(output_type='NIFTI_GZ'),
name="segmentation", mem_gb=4)
# Select WM segmentation file from segmentation output
def get_wm(files):
return files[-1]
# Threshold - Threshold WM probability image
threshold = Node(Threshold(thresh=0.5,
args='-bin',
output_type='NIFTI_GZ'),
name="threshold")
# FLIRT - pre-alignment of functional images to anatomical images
coreg_pre = Node(FLIRT(dof=6, output_type='NIFTI_GZ'),
name="coreg_pre")
# FLIRT - coregistration of functional images to anatomical images with BBR
coreg_bbr = Node(FLIRT(dof=6,
cost='bbr',
schedule=opj(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch'),
output_type='NIFTI_GZ'),
name="coreg_bbr")
# Apply coregistration warp to functional images
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI'),
name="applywarp")
# Apply coregistration warp to mean file
applywarp_mean = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI_GZ'),
name="applywarp_mean")
# Create a coregistration workflow
coregwf = Workflow(name='coregwf')
coregwf.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the coregistration workflow
coregwf.connect([(bet_anat, segmentation, [('out_file', 'in_files')]),
(segmentation, threshold, [(('partial_volume_files', get_wm),
'in_file')]),
(bet_anat, coreg_pre, [('out_file', 'reference')]),
(threshold, coreg_bbr, [('out_file', 'wm_seg')]),
(coreg_pre, coreg_bbr, [('out_matrix_file', 'in_matrix_file')]),
(coreg_bbr, applywarp, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp, [('out_file', 'reference')]),
(coreg_bbr, applywarp_mean, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp_mean, [('out_file', 'reference')]),
])
Specify input & output stream¶
Specify where the input data can be found & where and how to save the output data.
# Infosource - a function free node to iterate over the list of subject names
infosource = Node(IdentityInterface(fields=['subject_id', 'task_name']),
name="infosource")
infosource.iterables = [('subject_id', subject_list),
('task_name', task_list)]
# SelectFiles - to grab the data (alternativ to DataGrabber)
anat_file = opj('derivatives', 'fmriprep', 'sub-{subject_id}', 'anat', 'sub-{subject_id}_t1w_preproc.nii.gz')
func_file = opj('sub-{subject_id}', 'ses-test', 'func',
'sub-{subject_id}_ses-test_task-{task_name}_bold.nii.gz')
templates = {'anat': anat_file,
'func': func_file}
selectfiles = Node(SelectFiles(templates,
base_directory='/home/neuro/workshop/data/ds000114'),
name="selectfiles")
# Datasink - creates output folder for important outputs
datasink = Node(DataSink(base_directory=experiment_dir,
container=output_dir),
name="datasink")
## Use the following DataSink output substitutions
substitutions = [('_subject_id_', 'sub-'),
('_task_name_', '/task-'),
('_fwhm_', 'fwhm-'),
('_roi', ''),
('_mcf', ''),
('_st', ''),
('_flirt', ''),
('.nii_mean_reg', '_mean'),
('.nii.par', '.par'),
]
subjFolders = [('fwhm-%s/' % f, 'fwhm-%s_' % f) for f in fwhm]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
Specify Workflow¶
Create a workflow and connect the interface nodes and the I/O stream to each other.
# Create a preprocessing workflow
preproc = Workflow(name='preproc')
preproc.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the preprocessing workflow
preproc.connect([(infosource, selectfiles, [('subject_id', 'subject_id'),
('task_name', 'task_name')]),
(selectfiles, extract, [('func', 'in_file')]),
(extract, mcflirt, [('roi_file', 'in_file')]),
(mcflirt, slicetimer, [('out_file', 'in_file')]),
(selectfiles, coregwf, [('anat', 'bet_anat.in_file'),
('anat', 'coreg_bbr.reference')]),
(mcflirt, coregwf, [('mean_img', 'coreg_pre.in_file'),
('mean_img', 'coreg_bbr.in_file'),
('mean_img', 'applywarp_mean.in_file')]),
(slicetimer, coregwf, [('slice_time_corrected_file', 'applywarp.in_file')]),
(coregwf, smooth, [('applywarp.out_file', 'in_files')]),
(mcflirt, datasink, [('par_file', 'preproc.@par')]),
(smooth, datasink, [('smoothed_files', 'preproc.@smooth')]),
(coregwf, datasink, [('applywarp_mean.out_file', 'preproc.@mean')]),
(coregwf, art, [('applywarp.out_file', 'realigned_files')]),
(mcflirt, art, [('par_file', 'realignment_parameters')]),
(coregwf, datasink, [('coreg_bbr.out_matrix_file', 'preproc.@mat_file'),
('bet_anat.out_file', 'preproc.@brain')]),
(art, datasink, [('outlier_files', 'preproc.@outlier_files'),
('plot_files', 'preproc.@plot_files')]),
])
Visualize the workflow¶
It always helps to visualize your workflow.
# Create preproc output graph
preproc.write_graph(graph2use='colored', format='png', simple_form=True)
# Visualize the graph
from IPython.display import Image
Image(filename=opj(preproc.base_dir, 'preproc', 'graph.png'))
211018-10:44:02,519 nipype.workflow INFO:
Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=colored, simple_form=True).
# Visualize the detailed graph
preproc.write_graph(graph2use='flat', format='png', simple_form=True)
Image(filename=opj(preproc.base_dir, 'preproc', 'graph_detailed.png'))
211018-10:44:03,57 nipype.workflow INFO:
Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=flat, simple_form=True).
Run the Workflow¶
Now that everything is ready, we can run the preprocessing workflow. Change n_procs to the number of jobs/cores you want to use. Note that if you’re using a Docker container and FLIRT fails to run without any good reason, you might need to change memory settings in the Docker preferences (6 GB should be enough for this workflow).
preproc.run('MultiProc', plugin_args={'n_procs': 4})
211018-10:44:03,104 nipype.workflow INFO:
Workflow preproc settings: ['check', 'execution', 'logging', 'monitoring']
211018-10:44:03,244 nipype.workflow INFO:
Running in parallel.
211018-10:44:03,254 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 10 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-10:44:03,364 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles".
211018-10:44:03,364 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles".
211018-10:44:03,364 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles".
211018-10:44:03,364 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles".
211018-10:44:03,376 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:44:03,377 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:44:03,384 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:44:03,379 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:44:03,389 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:44:03,397 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:44:03,398 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:44:03,405 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:44:05,265 nipype.workflow INFO:
[Job 0] Completed (preproc.selectfiles).
211018-10:44:05,269 nipype.workflow INFO:
[Job 16] Completed (preproc.selectfiles).
211018-10:44:05,271 nipype.workflow INFO:
[Job 32] Completed (preproc.selectfiles).
211018-10:44:05,273 nipype.workflow INFO:
[Job 48] Completed (preproc.selectfiles).
211018-10:44:05,277 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 14 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-10:44:05,388 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat".
211018-10:44:05,391 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract".
211018-10:44:05,393 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat".
211018-10:44:05,393 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract".
211018-10:44:05,403 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:44:05,409 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:44:05,415 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:44:05,416 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:44:06,280 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:44:06,280 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:44:07,262 nipype.workflow INFO:
[Job 4] Completed (preproc.extract).
211018-10:44:07,264 nipype.workflow INFO:
[Job 20] Completed (preproc.extract).
211018-10:44:07,268 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 4.83/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
211018-10:44:07,342 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt".
211018-10:44:07,342 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt".
211018-10:44:07,353 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:44:07,360 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:44:09,265 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 4.43/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.bet_anat
* preproc.coregwf.bet_anat
211018-10:44:20,425 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:44:20,583 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:44:21,278 nipype.workflow INFO:
[Job 1] Completed (preproc.coregwf.bet_anat).
211018-10:44:21,280 nipype.workflow INFO:
[Job 17] Completed (preproc.coregwf.bet_anat).
211018-10:44:21,283 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 4.83/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
211018-10:44:21,340 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation".
211018-10:44:21,342 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat".
211018-10:44:21,350 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain.nii.gz
211018-10:44:21,355 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:44:23,308 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
211018-10:44:38,642 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:44:39,310 nipype.workflow INFO:
[Job 33] Completed (preproc.coregwf.bet_anat).
211018-10:44:39,314 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
211018-10:44:39,389 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract".
211018-10:44:39,399 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:44:40,105 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:44:41,313 nipype.workflow INFO:
[Job 36] Completed (preproc.extract).
211018-10:44:41,317 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
211018-10:44:41,377 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt".
211018-10:44:41,386 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:44:43,317 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.mcflirt
* preproc.mcflirt
211018-10:45:29,247 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:45:29,466 nipype.workflow INFO:
[Job 5] Completed (preproc.mcflirt).
211018-10:45:29,476 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 12 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.mcflirt
211018-10:45:29,590 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre".
211018-10:45:29,611 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:45:31,477 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 11 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.mcflirt
211018-10:45:33,888 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:45:35,469 nipype.workflow INFO:
[Job 21] Completed (preproc.mcflirt).
211018-10:45:35,474 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 13 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:35,536 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer".
211018-10:45:35,549 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:45:37,474 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 12 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:40,562 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:45:40,738 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:45:41,476 nipype.workflow INFO:
[Job 6] Completed (preproc.coregwf.coreg_pre).
211018-10:45:41,477 nipype.workflow INFO:
[Job 9] Completed (preproc.slicetimer).
211018-10:45:41,481 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:41,539 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre".
211018-10:45:41,539 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer".
211018-10:45:41,551 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:45:41,554 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:45:43,479 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:46,400 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:45:47,482 nipype.workflow INFO:
[Job 25] Completed (preproc.slicetimer).
211018-10:45:47,486 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:47,548 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat".
211018-10:45:47,558 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:45:49,485 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:53,258 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:45:53,593 nipype.workflow INFO:
[Job 22] Completed (preproc.coregwf.coreg_pre).
211018-10:45:53,610 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:53,741 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract".
211018-10:45:53,766 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:45:54,983 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:45:55,560 nipype.workflow INFO:
[Job 52] Completed (preproc.extract).
211018-10:45:55,563 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:55,627 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt".
211018-10:45:55,644 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:45:57,489 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:45:57,562 nipype.workflow INFO:
[Job 49] Completed (preproc.coregwf.bet_anat).
211018-10:45:57,566 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:57,630 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles".
211018-10:45:57,636 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:45:57,645 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:45:59,564 nipype.workflow INFO:
[Job 64] Completed (preproc.selectfiles).
211018-10:45:59,568 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:45:59,629 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat".
211018-10:45:59,637 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:46:01,570 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:07,810 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:46:09,576 nipype.workflow INFO:
[Job 37] Completed (preproc.mcflirt).
211018-10:46:09,579 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:09,656 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre".
211018-10:46:09,667 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:46:11,580 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:14,25 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:46:15,581 nipype.workflow INFO:
[Job 65] Completed (preproc.coregwf.bet_anat).
211018-10:46:15,586 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:15,654 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer".
211018-10:46:15,663 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:46:17,586 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:19,793 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:46:20,110 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:46:21,588 nipype.workflow INFO:
[Job 38] Completed (preproc.coregwf.coreg_pre).
211018-10:46:21,590 nipype.workflow INFO:
[Job 41] Completed (preproc.slicetimer).
211018-10:46:21,593 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:21,654 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract".
211018-10:46:21,654 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles".
211018-10:46:21,660 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:46:21,665 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:46:21,666 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:46:22,257 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:46:23,589 nipype.workflow INFO:
[Job 68] Completed (preproc.extract).
211018-10:46:23,591 nipype.workflow INFO:
[Job 80] Completed (preproc.selectfiles).
211018-10:46:23,594 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 11 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:23,649 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt".
211018-10:46:23,649 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat".
211018-10:46:23,658 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:46:23,659 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:46:25,594 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:36,837 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:46:37,604 nipype.workflow INFO:
[Job 81] Completed (preproc.coregwf.bet_anat).
211018-10:46:37,609 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:37,671 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract".
211018-10:46:37,679 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:46:38,345 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:46:39,606 nipype.workflow INFO:
[Job 84] Completed (preproc.extract).
211018-10:46:39,609 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:46:39,671 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt".
211018-10:46:39,678 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:46:41,611 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:08,188 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:47:09,641 nipype.workflow INFO:
[Job 53] Completed (preproc.mcflirt).
211018-10:47:09,645 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:09,706 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre".
211018-10:47:09,725 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:47:11,644 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:17,832 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:47:19,652 nipype.workflow INFO:
[Job 54] Completed (preproc.coregwf.coreg_pre).
211018-10:47:19,655 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:19,715 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer".
211018-10:47:19,727 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:47:21,657 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:24,559 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:47:25,659 nipype.workflow INFO:
[Job 57] Completed (preproc.slicetimer).
211018-10:47:25,663 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:25,750 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles".
211018-10:47:25,780 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:47:25,797 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:47:27,662 nipype.workflow INFO:
[Job 96] Completed (preproc.selectfiles).
211018-10:47:27,665 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:27,744 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat".
211018-10:47:27,762 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:47:29,666 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:38,631 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:47:39,675 nipype.workflow INFO:
[Job 69] Completed (preproc.mcflirt).
211018-10:47:39,678 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:39,740 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre".
211018-10:47:39,752 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:47:40,704 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:47:41,677 nipype.workflow INFO:
[Job 97] Completed (preproc.coregwf.bet_anat).
211018-10:47:41,681 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:41,740 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer".
211018-10:47:41,752 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:47:43,681 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:45,692 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:47:47,682 nipype.workflow INFO:
[Job 73] Completed (preproc.slicetimer).
211018-10:47:47,688 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:47,748 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract".
211018-10:47:47,758 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:47:48,532 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:47:48,694 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:47:49,685 nipype.workflow INFO:
[Job 70] Completed (preproc.coregwf.coreg_pre).
211018-10:47:49,686 nipype.workflow INFO:
[Job 100] Completed (preproc.extract).
211018-10:47:49,690 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 10 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:49,767 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt".
211018-10:47:49,769 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles".
211018-10:47:49,776 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:47:49,785 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:47:49,796 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:47:51,232 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:47:51,686 nipype.workflow INFO:
[Job 85] Completed (preproc.mcflirt).
211018-10:47:51,688 nipype.workflow INFO:
[Job 112] Completed (preproc.selectfiles).
211018-10:47:51,691 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 12 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:47:51,747 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre".
211018-10:47:51,748 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer".
211018-10:47:51,760 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:47:51,762 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:47:52,969 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-10:47:53,689 nipype.workflow INFO:
[Job 2] Completed (preproc.coregwf.segmentation).
211018-10:47:53,695 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 4.63/5.23, Free processors: 1/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
211018-10:47:53,755 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold".
211018-10:47:53,772 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:47:54,699 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-10:47:55,691 nipype.workflow INFO:
[Job 3] Completed (preproc.coregwf.threshold).
211018-10:47:55,695 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 4.63/5.23, Free processors: 1/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.mcflirt
211018-10:47:55,764 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr".
211018-10:47:55,795 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:47:55,875 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:47:57,694 nipype.workflow INFO:
[Job 89] Completed (preproc.slicetimer).
211018-10:47:57,696 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 4.63/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_pre
* preproc.mcflirt
211018-10:47:57,769 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation".
211018-10:47:57,779 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain.nii.gz
211018-10:47:59,697 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.coregwf.coreg_pre
* preproc.mcflirt
211018-10:48:00,994 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:48:01,697 nipype.workflow INFO:
[Job 86] Completed (preproc.coregwf.coreg_pre).
211018-10:48:01,700 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
211018-10:48:01,786 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat".
211018-10:48:01,795 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:48:03,701 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
211018-10:48:22,814 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:48:23,721 nipype.workflow INFO:
[Job 113] Completed (preproc.coregwf.bet_anat).
211018-10:48:23,725 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
211018-10:48:23,813 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract".
211018-10:48:23,825 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:48:24,443 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:48:25,727 nipype.workflow INFO:
[Job 116] Completed (preproc.extract).
211018-10:48:25,733 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
211018-10:48:25,896 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt".
211018-10:48:25,906 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:48:27,731 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
* preproc.mcflirt
211018-10:48:57,462 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:48:57,762 nipype.workflow INFO:
[Job 101] Completed (preproc.mcflirt).
211018-10:48:57,766 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:48:57,846 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre".
211018-10:48:57,859 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:48:59,768 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:07,85 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:49:07,773 nipype.workflow INFO:
[Job 102] Completed (preproc.coregwf.coreg_pre).
211018-10:49:07,777 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:07,839 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer".
211018-10:49:07,851 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:49:09,777 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:11,836 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:49:13,779 nipype.workflow INFO:
[Job 105] Completed (preproc.slicetimer).
211018-10:49:13,786 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 8 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:13,859 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles".
211018-10:49:13,865 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:49:13,872 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:49:15,781 nipype.workflow INFO:
[Job 128] Completed (preproc.selectfiles).
211018-10:49:15,785 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:15,843 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat".
211018-10:49:15,852 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:49:17,786 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:34,216 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:49:35,800 nipype.workflow INFO:
[Job 129] Completed (preproc.coregwf.bet_anat).
211018-10:49:35,804 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:35,864 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract".
211018-10:49:35,873 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:49:36,520 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:49:36,819 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:49:37,802 nipype.workflow INFO:
[Job 117] Completed (preproc.mcflirt).
211018-10:49:37,803 nipype.workflow INFO:
[Job 132] Completed (preproc.extract).
211018-10:49:37,807 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 11 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:37,860 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre".
211018-10:49:37,861 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer".
211018-10:49:37,871 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:49:37,871 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:49:39,807 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:42,55 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:49:43,808 nipype.workflow INFO:
[Job 121] Completed (preproc.slicetimer).
211018-10:49:43,811 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:43,868 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt".
211018-10:49:43,879 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:49:45,810 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:47,375 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:49:47,812 nipype.workflow INFO:
[Job 118] Completed (preproc.coregwf.coreg_pre).
211018-10:49:47,816 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 8 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:47,875 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles".
211018-10:49:47,881 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
211018-10:49:47,894 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
211018-10:49:49,814 nipype.workflow INFO:
[Job 144] Completed (preproc.selectfiles).
211018-10:49:49,817 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:49:49,873 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat".
211018-10:49:49,881 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -f 0.50 -R
211018-10:49:51,818 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.bet_anat
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:50:00,45 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
211018-10:50:01,831 nipype.workflow INFO:
[Job 145] Completed (preproc.coregwf.bet_anat).
211018-10:50:01,833 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:50:01,916 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract".
211018-10:50:01,924 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /home/neuro/workshop/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
211018-10:50:02,540 nipype.workflow INFO:
[Node] Finished "preproc.extract".
211018-10:50:03,833 nipype.workflow INFO:
[Job 148] Completed (preproc.extract).
211018-10:50:03,836 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:50:03,896 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt".
211018-10:50:03,906 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
211018-10:50:05,836 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_bbr
211018-10:50:11,790 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-10:50:11,841 nipype.workflow INFO:
[Job 7] Completed (preproc.coregwf.coreg_bbr).
211018-10:50:11,844 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:11,921 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp_mean".
211018-10:50:11,932 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:50:13,846 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.applywarp_mean
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:13,972 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-10:50:15,846 nipype.workflow INFO:
[Job 8] Completed (preproc.coregwf.applywarp_mean).
211018-10:50:15,849 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:15,906 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp".
211018-10:50:15,918 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:50:17,849 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:26,377 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-10:50:27,950 nipype.workflow INFO:
[Job 10] Completed (preproc.coregwf.applywarp).
211018-10:50:27,970 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:28,299 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/smooth".
211018-10:50:28,341 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:50:29,915 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 10 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:53,755 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:50:53,937 nipype.workflow INFO:
[Job 133] Completed (preproc.mcflirt).
211018-10:50:53,940 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 12 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:54,7 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/smooth".
211018-10:50:54,27 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:50:55,596 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:50:55,939 nipype.workflow INFO:
[Job 11] Completed (preproc.smooth).
211018-10:50:55,942 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:56,5 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/art".
211018-10:50:56,17 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-10:50:56,699 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-10:50:57,940 nipype.workflow INFO:
[Job 13] Completed (preproc.art).
211018-10:50:57,944 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 11 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:50:58,3 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/datasink".
211018-10:50:58,26 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:50:58,29 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par
211018-10:50:58,32 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:50:58,34 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
211018-10:50:58,37 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz
211018-10:50:58,40 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:50:58,43 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:50:58,49 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_8/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-8_ssub-10_ses-test_task-fingerfootlips_bold.nii
211018-10:50:58,65 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:50:59,943 nipype.workflow INFO:
[Job 14] Completed (preproc.datasink).
211018-10:50:59,946 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 10 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:51:00,7 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre".
211018-10:51:00,17 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:51:01,946 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 9 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.coregwf.coreg_pre
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:51:11,575 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:51:11,955 nipype.workflow INFO:
[Job 134] Completed (preproc.coregwf.coreg_pre).
211018-10:51:11,958 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 9 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:51:12,20 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer".
211018-10:51:12,29 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:51:13,960 nipype.workflow INFO:
[MultiProc] Running 4 tasks, and 8 jobs ready. Free memory (GB): 0.63/5.23, Free processors: 0/4.
Currently running:
* preproc.slicetimer
* preproc.smooth
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:51:16,81 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:51:17,457 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:51:17,962 nipype.workflow INFO:
[Job 12] Completed (preproc.smooth).
211018-10:51:17,963 nipype.workflow INFO:
[Job 137] Completed (preproc.slicetimer).
211018-10:51:17,966 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.mcflirt
* preproc.coregwf.segmentation
211018-10:51:18,21 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/datasink".
211018-10:51:18,40 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:51:18,43 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par
211018-10:51:18,45 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:51:18,48 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
211018-10:51:18,51 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz
211018-10:51:18,57 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:51:18,59 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:51:18,61 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_4/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-4_ssub-10_ses-test_task-fingerfootlips_bold.nii
211018-10:51:18,70 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:51:18,310 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
211018-10:51:19,964 nipype.workflow INFO:
[Job 149] Completed (preproc.mcflirt).
211018-10:51:19,965 nipype.workflow INFO:
[Job 15] Completed (preproc.datasink).
211018-10:51:19,968 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 10 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:51:20,24 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre".
211018-10:51:20,24 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer".
211018-10:51:20,43 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
211018-10:51:20,45 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
211018-10:51:21,967 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 8 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.slicetimer
* preproc.coregwf.coreg_pre
* preproc.coregwf.segmentation
211018-10:51:24,20 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
211018-10:51:24,55 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-10:51:25,970 nipype.workflow INFO:
[Job 18] Completed (preproc.coregwf.segmentation).
211018-10:51:25,972 nipype.workflow INFO:
[Job 153] Completed (preproc.slicetimer).
211018-10:51:25,975 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.coreg_pre
211018-10:51:26,30 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation".
211018-10:51:26,30 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold".
211018-10:51:26,38 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:51:26,39 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain.nii.gz
211018-10:51:26,861 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-10:51:27,972 nipype.workflow INFO:
[Job 19] Completed (preproc.coregwf.threshold).
211018-10:51:27,975 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.segmentation
* preproc.coregwf.coreg_pre
211018-10:51:28,28 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr".
211018-10:51:28,40 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:51:28,602 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
211018-10:51:29,974 nipype.workflow INFO:
[Job 150] Completed (preproc.coregwf.coreg_pre).
211018-10:51:29,977 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-10:53:25,597 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-10:53:26,87 nipype.workflow INFO:
[Job 23] Completed (preproc.coregwf.coreg_bbr).
211018-10:53:26,91 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:53:26,144 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp_mean".
211018-10:53:26,145 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp".
211018-10:53:26,156 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:53:26,156 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:53:28,95 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 7 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.coregwf.segmentation
211018-10:53:28,962 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-10:53:30,92 nipype.workflow INFO:
[Job 24] Completed (preproc.coregwf.applywarp_mean).
211018-10:53:30,97 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-10:53:36,857 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-10:53:38,99 nipype.workflow INFO:
[Job 26] Completed (preproc.coregwf.applywarp).
211018-10:53:38,102 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 10 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:53:38,155 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/smooth".
211018-10:53:38,155 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/smooth".
211018-10:53:38,157 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/art".
211018-10:53:38,165 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:53:38,168 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-10:53:38,167 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:53:38,711 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-10:53:40,102 nipype.workflow INFO:
[Job 29] Completed (preproc.art).
211018-10:53:40,106 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 7 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-10:53:59,243 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:53:59,566 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:54:00,123 nipype.workflow INFO:
[Job 27] Completed (preproc.smooth).
211018-10:54:00,125 nipype.workflow INFO:
[Job 28] Completed (preproc.smooth).
211018-10:54:00,128 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:54:00,188 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/datasink".
211018-10:54:00,187 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/datasink".
211018-10:54:00,207 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:54:00,207 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:54:00,209 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
211018-10:54:00,213 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
211018-10:54:00,213 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:54:00,217 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
211018-10:54:00,219 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
211018-10:54:00,215 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:54:00,221 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:54:00,224 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:54:00,224 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
211018-10:54:00,226 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
211018-10:54:00,228 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:54:00,228 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_8/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-8_ssub-09_ses-test_task-fingerfootlips_bold.nii
211018-10:54:00,230 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:54:00,232 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_4/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-4_ssub-09_ses-test_task-fingerfootlips_bold.nii
211018-10:54:00,237 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:54:00,240 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:54:02,125 nipype.workflow INFO:
[Job 30] Completed (preproc.datasink).
211018-10:54:02,127 nipype.workflow INFO:
[Job 31] Completed (preproc.datasink).
211018-10:54:02,130 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:54:15,797 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-10:54:16,144 nipype.workflow INFO:
[Job 34] Completed (preproc.coregwf.segmentation).
211018-10:54:16,149 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 8 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-10:54:16,213 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation".
211018-10:54:16,212 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold".
211018-10:54:16,224 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain.nii.gz
211018-10:54:16,224 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:54:17,68 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-10:54:18,144 nipype.workflow INFO:
[Job 35] Completed (preproc.coregwf.threshold).
211018-10:54:18,147 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:54:18,202 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr".
211018-10:54:18,228 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:54:20,147 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-10:56:13,964 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-10:56:14,272 nipype.workflow INFO:
[Job 39] Completed (preproc.coregwf.coreg_bbr).
211018-10:56:14,275 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:56:14,328 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp_mean".
211018-10:56:14,329 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp".
211018-10:56:14,339 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:56:14,340 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:56:16,145 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-10:56:16,275 nipype.workflow INFO:
[Job 40] Completed (preproc.coregwf.applywarp_mean).
211018-10:56:16,278 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-10:56:23,485 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-10:56:24,283 nipype.workflow INFO:
[Job 42] Completed (preproc.coregwf.applywarp).
211018-10:56:24,286 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:56:24,340 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/smooth".
211018-10:56:24,340 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/smooth".
211018-10:56:24,340 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/art".
211018-10:56:24,347 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:56:24,348 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:56:24,350 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-10:56:24,863 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-10:56:26,286 nipype.workflow INFO:
[Job 45] Completed (preproc.art).
211018-10:56:26,292 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 6 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-10:56:45,747 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:56:45,896 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:56:46,301 nipype.workflow INFO:
[Job 43] Completed (preproc.smooth).
211018-10:56:46,304 nipype.workflow INFO:
[Job 44] Completed (preproc.smooth).
211018-10:56:46,308 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:56:46,361 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/datasink".
211018-10:56:46,363 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/datasink".
211018-10:56:46,381 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:56:46,381 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:56:46,383 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
211018-10:56:46,387 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
211018-10:56:46,387 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:56:46,389 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:56:46,390 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
211018-10:56:46,391 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
211018-10:56:46,393 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:56:46,394 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
211018-10:56:46,395 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
211018-10:56:46,397 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:56:46,398 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:56:46,400 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:56:46,398 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_8/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-8_ssub-08_ses-test_task-fingerfootlips_bold.nii
211018-10:56:46,402 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_4/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-4_ssub-08_ses-test_task-fingerfootlips_bold.nii
211018-10:56:46,406 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:56:46,407 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:56:48,303 nipype.workflow INFO:
[Job 46] Completed (preproc.datasink).
211018-10:56:48,305 nipype.workflow INFO:
[Job 47] Completed (preproc.datasink).
211018-10:56:48,307 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:56:57,28 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-10:56:58,320 nipype.workflow INFO:
[Job 50] Completed (preproc.coregwf.segmentation).
211018-10:56:58,325 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 7 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-10:56:58,389 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold".
211018-10:56:58,389 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation".
211018-10:56:58,401 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain.nii.gz
211018-10:56:58,402 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:56:59,200 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-10:57:00,320 nipype.workflow INFO:
[Job 51] Completed (preproc.coregwf.threshold).
211018-10:57:00,324 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:57:00,375 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr".
211018-10:57:00,398 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:57:02,323 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-10:59:08,380 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-10:59:08,468 nipype.workflow INFO:
[Job 55] Completed (preproc.coregwf.coreg_bbr).
211018-10:59:08,470 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:59:08,523 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp_mean".
211018-10:59:08,523 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp".
211018-10:59:08,534 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:59:08,539 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-10:59:10,430 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-10:59:10,470 nipype.workflow INFO:
[Job 56] Completed (preproc.coregwf.applywarp_mean).
211018-10:59:10,473 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-10:59:17,976 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-10:59:18,480 nipype.workflow INFO:
[Job 58] Completed (preproc.coregwf.applywarp).
211018-10:59:18,484 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:59:18,570 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/smooth".
211018-10:59:18,570 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/smooth".
211018-10:59:18,572 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/art".
211018-10:59:18,582 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:59:18,583 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-10:59:18,590 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-10:59:19,304 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-10:59:20,482 nipype.workflow INFO:
[Job 61] Completed (preproc.art).
211018-10:59:20,486 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-10:59:43,693 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-10:59:44,506 nipype.workflow INFO:
[Job 66] Completed (preproc.coregwf.segmentation).
211018-10:59:44,510 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 4.83/5.23, Free processors: 2/4.
Currently running:
* preproc.smooth
* preproc.smooth
211018-10:59:44,570 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation".
211018-10:59:44,570 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold".
211018-10:59:44,580 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain.nii.gz
211018-10:59:44,584 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:59:45,506 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-10:59:45,844 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:59:46,312 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-10:59:46,509 nipype.workflow INFO:
[Job 59] Completed (preproc.smooth).
211018-10:59:46,511 nipype.workflow INFO:
[Job 60] Completed (preproc.smooth).
211018-10:59:46,512 nipype.workflow INFO:
[Job 67] Completed (preproc.coregwf.threshold).
211018-10:59:46,516 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-10:59:46,589 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/datasink".
211018-10:59:46,594 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr".
211018-10:59:46,594 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/datasink".
211018-10:59:46,614 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-10:59:46,626 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:59:46,626 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-10:59:46,629 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
211018-10:59:46,631 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:59:46,634 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
211018-10:59:46,633 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
211018-10:59:46,636 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
211018-10:59:46,639 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
211018-10:59:46,641 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:59:46,644 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
211018-10:59:46,644 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:59:46,646 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
211018-10:59:46,648 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_4/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-4_ssub-07_ses-test_task-fingerfootlips_bold.nii
211018-10:59:46,655 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:59:46,651 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
211018-10:59:46,658 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-10:59:46,660 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_8/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-8_ssub-07_ses-test_task-fingerfootlips_bold.nii
211018-10:59:46,667 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-10:59:48,511 nipype.workflow INFO:
[Job 62] Completed (preproc.datasink).
211018-10:59:48,513 nipype.workflow INFO:
[Job 63] Completed (preproc.datasink).
211018-10:59:48,516 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-11:01:19,479 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:01:20,606 nipype.workflow INFO:
[Job 71] Completed (preproc.coregwf.coreg_bbr).
211018-11:01:20,609 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:01:20,661 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp_mean".
211018-11:01:20,661 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp".
211018-11:01:20,676 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:01:20,678 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:01:22,610 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.coregwf.segmentation
211018-11:01:22,982 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:01:24,611 nipype.workflow INFO:
[Job 72] Completed (preproc.coregwf.applywarp_mean).
211018-11:01:24,614 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-11:01:31,878 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:01:32,619 nipype.workflow INFO:
[Job 74] Completed (preproc.coregwf.applywarp).
211018-11:01:32,622 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:01:32,676 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:01:32,678 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:01:32,679 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/art".
211018-11:01:32,688 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:01:32,688 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:01:32,685 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:01:33,192 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:01:34,621 nipype.workflow INFO:
[Job 77] Completed (preproc.art).
211018-11:01:34,625 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-11:01:55,988 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:01:56,423 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:01:56,643 nipype.workflow INFO:
[Job 75] Completed (preproc.smooth).
211018-11:01:56,645 nipype.workflow INFO:
[Job 76] Completed (preproc.smooth).
211018-11:01:56,648 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:01:56,706 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:01:56,707 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:01:56,729 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:01:56,728 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:01:56,731 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
211018-11:01:56,732 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
211018-11:01:56,735 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:01:56,735 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:01:56,738 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg
211018-11:01:56,740 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
211018-11:01:56,744 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:01:56,743 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg
211018-11:01:56,746 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
211018-11:01:56,749 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:01:56,751 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:01:56,751 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_8/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-8_ssub-06_ses-test_task-fingerfootlips_bold.nii
211018-11:01:56,754 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:01:56,757 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_4/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-4_ssub-06_ses-test_task-fingerfootlips_bold.nii
211018-11:01:56,760 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:01:56,762 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:01:58,645 nipype.workflow INFO:
[Job 78] Completed (preproc.datasink).
211018-11:01:58,648 nipype.workflow INFO:
[Job 79] Completed (preproc.datasink).
211018-11:01:58,650 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:02:45,765 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-11:02:46,701 nipype.workflow INFO:
[Job 82] Completed (preproc.coregwf.segmentation).
211018-11:02:46,709 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 5 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:02:46,771 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold".
211018-11:02:46,777 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation".
211018-11:02:46,803 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:02:46,803 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain.nii.gz
211018-11:02:47,616 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-11:02:48,701 nipype.workflow INFO:
[Job 83] Completed (preproc.coregwf.threshold).
211018-11:02:48,705 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:02:48,770 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr".
211018-11:02:48,785 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:02:50,704 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-11:04:35,992 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:04:36,817 nipype.workflow INFO:
[Job 87] Completed (preproc.coregwf.coreg_bbr).
211018-11:04:36,821 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:04:36,876 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp_mean".
211018-11:04:36,877 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp".
211018-11:04:36,887 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:04:36,887 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:04:38,611 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:04:38,819 nipype.workflow INFO:
[Job 88] Completed (preproc.coregwf.applywarp_mean).
211018-11:04:38,823 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-11:04:45,744 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:04:46,828 nipype.workflow INFO:
[Job 90] Completed (preproc.coregwf.applywarp).
211018-11:04:46,830 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:04:46,886 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:04:46,887 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/art".
211018-11:04:46,885 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:04:46,895 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:04:46,899 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:04:46,899 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:04:47,343 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:04:48,830 nipype.workflow INFO:
[Job 93] Completed (preproc.art).
211018-11:04:48,834 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-11:05:07,937 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:05:08,187 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:05:08,847 nipype.workflow INFO:
[Job 91] Completed (preproc.smooth).
211018-11:05:08,849 nipype.workflow INFO:
[Job 92] Completed (preproc.smooth).
211018-11:05:08,852 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:05:08,909 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:05:08,911 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:05:08,941 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:05:08,941 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:05:08,946 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
211018-11:05:08,944 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
211018-11:05:08,949 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:05:08,951 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:05:08,953 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
211018-11:05:08,956 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
211018-11:05:08,961 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
211018-11:05:08,960 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
211018-11:05:08,965 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:05:08,964 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:05:08,970 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:05:08,967 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:05:08,976 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_4/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-4_ssub-05_ses-test_task-fingerfootlips_bold.nii
211018-11:05:08,982 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_8/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-8_ssub-05_ses-test_task-fingerfootlips_bold.nii
211018-11:05:08,989 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:05:08,990 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:05:10,849 nipype.workflow INFO:
[Job 94] Completed (preproc.datasink).
211018-11:05:10,850 nipype.workflow INFO:
[Job 95] Completed (preproc.datasink).
211018-11:05:10,853 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:05:36,460 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-11:05:36,882 nipype.workflow INFO:
[Job 98] Completed (preproc.coregwf.segmentation).
211018-11:05:36,887 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:05:36,947 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold".
211018-11:05:36,948 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation".
211018-11:05:36,958 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain.nii.gz
211018-11:05:36,958 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:05:37,763 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-11:05:38,882 nipype.workflow INFO:
[Job 99] Completed (preproc.coregwf.threshold).
211018-11:05:38,884 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:05:38,945 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr".
211018-11:05:38,962 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:05:40,885 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-11:07:16,701 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:07:16,986 nipype.workflow INFO:
[Job 103] Completed (preproc.coregwf.coreg_bbr).
211018-11:07:16,988 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:07:17,42 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp_mean".
211018-11:07:17,42 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp".
211018-11:07:17,54 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:07:17,53 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:07:18,814 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:07:18,988 nipype.workflow INFO:
[Job 104] Completed (preproc.coregwf.applywarp_mean).
211018-11:07:18,992 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-11:07:26,241 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:07:26,997 nipype.workflow INFO:
[Job 106] Completed (preproc.coregwf.applywarp).
211018-11:07:26,999 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:07:27,53 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:07:27,53 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:07:27,54 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/art".
211018-11:07:27,62 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:07:27,63 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:07:27,72 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:07:27,528 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:07:28,999 nipype.workflow INFO:
[Job 109] Completed (preproc.art).
211018-11:07:29,2 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-11:07:49,664 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:07:49,814 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:07:51,22 nipype.workflow INFO:
[Job 107] Completed (preproc.smooth).
211018-11:07:51,24 nipype.workflow INFO:
[Job 108] Completed (preproc.smooth).
211018-11:07:51,27 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:07:51,112 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:07:51,112 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:07:51,147 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:07:51,147 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:07:51,150 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
211018-11:07:51,153 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
211018-11:07:51,155 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:07:51,158 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:07:51,160 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
211018-11:07:51,162 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
211018-11:07:51,162 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
211018-11:07:51,165 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:07:51,168 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:07:51,166 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
211018-11:07:51,173 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_8/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-8_ssub-04_ses-test_task-fingerfootlips_bold.nii
211018-11:07:51,174 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:07:51,179 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:07:51,177 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:07:51,182 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_4/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-4_ssub-04_ses-test_task-fingerfootlips_bold.nii
211018-11:07:51,188 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:07:53,24 nipype.workflow INFO:
[Job 110] Completed (preproc.datasink).
211018-11:07:53,26 nipype.workflow INFO:
[Job 111] Completed (preproc.datasink).
211018-11:07:53,29 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:08:45,970 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-11:08:47,98 nipype.workflow INFO:
[Job 114] Completed (preproc.coregwf.segmentation).
211018-11:08:47,103 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:08:47,164 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold".
211018-11:08:47,165 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation".
211018-11:08:47,176 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:08:47,175 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain.nii.gz
211018-11:08:47,974 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-11:08:49,98 nipype.workflow INFO:
[Job 115] Completed (preproc.coregwf.threshold).
211018-11:08:49,103 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:08:49,184 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr".
211018-11:08:49,207 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:08:51,102 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-11:11:49,450 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:11:51,302 nipype.workflow INFO:
[Job 119] Completed (preproc.coregwf.coreg_bbr).
211018-11:11:51,305 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:11:51,369 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp".
211018-11:11:51,369 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp_mean".
211018-11:11:51,382 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:11:51,383 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:11:53,143 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:11:53,304 nipype.workflow INFO:
[Job 120] Completed (preproc.coregwf.applywarp_mean).
211018-11:11:53,307 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-11:12:00,110 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:12:01,313 nipype.workflow INFO:
[Job 122] Completed (preproc.coregwf.applywarp).
211018-11:12:01,319 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:12:01,397 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:12:01,397 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:12:01,399 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/art".
211018-11:12:01,412 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:12:01,418 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:12:01,429 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:12:02,24 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:12:03,315 nipype.workflow INFO:
[Job 125] Completed (preproc.art).
211018-11:12:03,319 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.segmentation
211018-11:12:21,441 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:12:21,960 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:12:23,336 nipype.workflow INFO:
[Job 123] Completed (preproc.smooth).
211018-11:12:23,338 nipype.workflow INFO:
[Job 124] Completed (preproc.smooth).
211018-11:12:23,343 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:12:23,399 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:12:23,399 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:12:23,418 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:12:23,418 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:12:23,419 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
211018-11:12:23,420 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
211018-11:12:23,422 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:12:23,425 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
211018-11:12:23,427 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:12:23,426 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
211018-11:12:23,429 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
211018-11:12:23,432 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
211018-11:12:23,431 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:12:23,434 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:12:23,437 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_8/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-8_ssub-03_ses-test_task-fingerfootlips_bold.nii
211018-11:12:23,435 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:12:23,439 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:12:23,442 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_4/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-4_ssub-03_ses-test_task-fingerfootlips_bold.nii
211018-11:12:23,450 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:12:23,451 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:12:25,338 nipype.workflow INFO:
[Job 126] Completed (preproc.datasink).
211018-11:12:25,340 nipype.workflow INFO:
[Job 127] Completed (preproc.datasink).
211018-11:12:25,342 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:13:07,915 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-11:13:09,399 nipype.workflow INFO:
[Job 130] Completed (preproc.coregwf.segmentation).
211018-11:13:09,406 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:13:09,466 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold".
211018-11:13:09,467 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation".
211018-11:13:09,480 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain.nii.gz
211018-11:13:09,480 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:13:10,715 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-11:13:11,399 nipype.workflow INFO:
[Job 131] Completed (preproc.coregwf.threshold).
211018-11:13:11,402 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:13:11,477 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr".
211018-11:13:11,505 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:13:13,402 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.coreg_bbr
* preproc.coregwf.segmentation
211018-11:16:24,216 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:16:24,622 nipype.workflow INFO:
[Job 135] Completed (preproc.coregwf.coreg_bbr).
211018-11:16:24,627 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 1.23/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.segmentation
211018-11:16:24,724 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp_mean".
211018-11:16:24,735 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp".
211018-11:16:24,758 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:16:24,774 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:16:26,625 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 0.83/5.23, Free processors: 1/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
* preproc.coregwf.segmentation
211018-11:16:28,752 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:16:30,627 nipype.workflow INFO:
[Job 136] Completed (preproc.coregwf.applywarp_mean).
211018-11:16:30,634 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 1.03/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.segmentation
211018-11:16:35,81 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
211018-11:16:36,635 nipype.workflow INFO:
[Job 146] Completed (preproc.coregwf.segmentation).
211018-11:16:36,641 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.applywarp
211018-11:16:36,746 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold".
211018-11:16:36,774 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:16:37,801 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
211018-11:16:38,637 nipype.workflow INFO:
[Job 147] Completed (preproc.coregwf.threshold).
211018-11:16:38,641 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.applywarp
211018-11:16:38,719 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr".
211018-11:16:38,753 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
211018-11:16:40,88 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:16:40,638 nipype.workflow INFO:
[Job 138] Completed (preproc.coregwf.applywarp).
211018-11:16:40,641 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.coreg_bbr
211018-11:16:40,714 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:16:40,714 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/art".
211018-11:16:40,713 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:16:40,730 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:16:40,733 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:16:40,732 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:16:41,557 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:16:42,640 nipype.workflow INFO:
[Job 141] Completed (preproc.art).
211018-11:16:42,647 nipype.workflow INFO:
[MultiProc] Running 3 tasks, and 0 jobs ready. Free memory (GB): 4.63/5.23, Free processors: 1/4.
Currently running:
* preproc.smooth
* preproc.smooth
* preproc.coregwf.coreg_bbr
211018-11:17:15,403 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:17:15,638 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:17:16,678 nipype.workflow INFO:
[Job 139] Completed (preproc.smooth).
211018-11:17:16,680 nipype.workflow INFO:
[Job 140] Completed (preproc.smooth).
211018-11:17:16,685 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.coreg_bbr
211018-11:17:16,765 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:17:16,765 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:17:16,799 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:17:16,800 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:17:16,803 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
211018-11:17:16,810 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:17:16,812 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
211018-11:17:16,812 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
211018-11:17:16,815 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
211018-11:17:16,816 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:17:16,818 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:17:16,822 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_8/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-8_ssub-02_ses-test_task-fingerfootlips_bold.nii
211018-11:17:16,831 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:17:16,834 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:17:16,837 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
211018-11:17:16,840 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
211018-11:17:16,847 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:17:16,851 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:17:16,854 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_4/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-4_ssub-02_ses-test_task-fingerfootlips_bold.nii
211018-11:17:16,864 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:17:18,680 nipype.workflow INFO:
[Job 142] Completed (preproc.datasink).
211018-11:17:18,682 nipype.workflow INFO:
[Job 143] Completed (preproc.datasink).
211018-11:17:18,686 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.coreg_bbr
211018-11:19:04,323 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
211018-11:19:04,796 nipype.workflow INFO:
[Job 151] Completed (preproc.coregwf.coreg_bbr).
211018-11:19:04,801 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:19:04,876 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp".
211018-11:19:04,878 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp_mean".
211018-11:19:04,907 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:19:04,907 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
211018-11:19:06,800 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 4.83/5.23, Free processors: 2/4.
Currently running:
* preproc.coregwf.applywarp
* preproc.coregwf.applywarp_mean
211018-11:19:07,217 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
211018-11:19:08,800 nipype.workflow INFO:
[Job 152] Completed (preproc.coregwf.applywarp_mean).
211018-11:19:08,804 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.coregwf.applywarp
211018-11:19:17,527 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
211018-11:19:18,812 nipype.workflow INFO:
[Job 154] Completed (preproc.coregwf.applywarp).
211018-11:19:18,816 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:19:18,891 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/smooth".
211018-11:19:18,891 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/smooth".
211018-11:19:18,893 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/art".
211018-11:19:18,908 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:19:18,909 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
211018-11:19:18,913 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
211018-11:19:19,675 nipype.workflow INFO:
[Node] Finished "preproc.art".
211018-11:19:20,813 nipype.workflow INFO:
[Job 157] Completed (preproc.art).
211018-11:19:20,817 nipype.workflow INFO:
[MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 4.83/5.23, Free processors: 2/4.
Currently running:
* preproc.smooth
* preproc.smooth
211018-11:19:50,789 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:19:50,852 nipype.workflow INFO:
[Job 156] Completed (preproc.smooth).
211018-11:19:50,856 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 5.03/5.23, Free processors: 3/4.
Currently running:
* preproc.smooth
211018-11:19:50,919 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/datasink".
211018-11:19:50,956 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:19:50,961 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
211018-11:19:50,966 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:19:50,970 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
211018-11:19:50,973 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
211018-11:19:50,978 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:19:50,981 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:19:50,985 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_4/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii
211018-11:19:50,991 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:19:51,114 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
211018-11:19:52,854 nipype.workflow INFO:
[Job 155] Completed (preproc.smooth).
211018-11:19:52,859 nipype.workflow INFO:
[Job 159] Completed (preproc.datasink).
211018-11:19:52,863 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
211018-11:19:52,929 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/datasink".
211018-11:19:52,956 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
211018-11:19:52,959 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
211018-11:19:52,960 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
211018-11:19:52,962 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
211018-11:19:52,965 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
211018-11:19:52,967 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
211018-11:19:52,969 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
211018-11:19:52,970 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_8/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii
211018-11:19:52,978 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
211018-11:19:54,859 nipype.workflow INFO:
[Job 158] Completed (preproc.datasink).
211018-11:19:54,862 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 5.23/5.23, Free processors: 4/4.
<networkx.classes.digraph.DiGraph at 0x7f8f22e36490>
Inspect output¶
Let’s check the structure of the output folder, to see if we have everything we wanted to save.
!tree /output/datasink/preproc
/output/datasink/preproc
├── sub-01
│ └── task-fingerfootlips
│ ├── art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-01_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-01_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-01_ses-test_task-fingerfootlips_bold.par
│ └── sub-01_t1w_preproc_brain.nii.gz
├── sub-02
│ └── task-fingerfootlips
│ ├── art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-02_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-02_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-02_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-02_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-02_ses-test_task-fingerfootlips_bold.par
│ └── sub-02_t1w_preproc_brain.nii.gz
├── sub-03
│ └── task-fingerfootlips
│ ├── art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-03_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-03_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-03_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-03_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-03_ses-test_task-fingerfootlips_bold.par
│ └── sub-03_t1w_preproc_brain.nii.gz
├── sub-04
│ └── task-fingerfootlips
│ ├── art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-04_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-04_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-04_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-04_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-04_ses-test_task-fingerfootlips_bold.par
│ └── sub-04_t1w_preproc_brain.nii.gz
├── sub-05
│ └── task-fingerfootlips
│ ├── art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-05_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-05_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-05_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-05_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-05_ses-test_task-fingerfootlips_bold.par
│ └── sub-05_t1w_preproc_brain.nii.gz
├── sub-06
│ └── task-fingerfootlips
│ ├── art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-06_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-06_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-06_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-06_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-06_ses-test_task-fingerfootlips_bold.par
│ └── sub-06_t1w_preproc_brain.nii.gz
├── sub-07
│ └── task-fingerfootlips
│ ├── art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-07_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-07_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-07_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-07_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-07_ses-test_task-fingerfootlips_bold.par
│ └── sub-07_t1w_preproc_brain.nii.gz
├── sub-08
│ └── task-fingerfootlips
│ ├── art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-08_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-08_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-08_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-08_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-08_ses-test_task-fingerfootlips_bold.par
│ └── sub-08_t1w_preproc_brain.nii.gz
├── sub-09
│ └── task-fingerfootlips
│ ├── art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
│ ├── fwhm-4_ssub-09_ses-test_task-fingerfootlips_bold.nii
│ ├── fwhm-8_ssub-09_ses-test_task-fingerfootlips_bold.nii
│ ├── plot.sub-09_ses-test_task-fingerfootlips_bold.svg
│ ├── sub-09_ses-test_task-fingerfootlips_bold_mean.mat
│ ├── sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
│ ├── sub-09_ses-test_task-fingerfootlips_bold.par
│ └── sub-09_t1w_preproc_brain.nii.gz
└── sub-10
└── task-fingerfootlips
├── art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
├── fwhm-4_ssub-10_ses-test_task-fingerfootlips_bold.nii
├── fwhm-8_ssub-10_ses-test_task-fingerfootlips_bold.nii
├── plot.sub-10_ses-test_task-fingerfootlips_bold.svg
├── sub-10_ses-test_task-fingerfootlips_bold_mean.mat
├── sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
├── sub-10_ses-test_task-fingerfootlips_bold.par
└── sub-10_t1w_preproc_brain.nii.gz
20 directories, 80 files
Visualize results¶
Let’s check the effect of the different smoothing kernels.
from nilearn import image, plotting
out_path = '/output/datasink/preproc/sub-01/task-fingerfootlips'
plotting.plot_epi(
'/home/neuro/workshop/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz',
title="T1", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
plotting.plot_epi(opj(out_path, 'sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz'),
title="fwhm = 0mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
plotting.plot_epi(image.mean_img(opj(out_path, 'fwhm-4_ssub-01_ses-test_task-fingerfootlips_bold.nii')),
title="fwhm = 4mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
plotting.plot_epi(image.mean_img(opj(out_path, 'fwhm-8_ssub-01_ses-test_task-fingerfootlips_bold.nii')),
title="fwhm = 8mm", display_mode='ortho', annotate=False, draw_cross=False, cmap='gray');
Now, let’s investigate the motion parameters. How much did the subject move and turn in the scanner?
import numpy as np
import matplotlib.pyplot as plt
par = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par')
fig, axes = plt.subplots(2, 1, figsize=(15, 5))
axes[0].set_ylabel('rotation (radians)')
axes[0].plot(par[0:, :3])
axes[1].plot(par[0:, 3:])
axes[1].set_xlabel('time (TR)')
axes[1].set_ylabel('translation (mm)');
There seems to be a rather drastic motion around volume 102. Let’s check if the outliers detection algorithm was able to pick this up.
import numpy as np
outlier_ids = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt')
print('Outliers were detected at volumes: %s' % outlier_ids)
from IPython.display import SVG
SVG(filename='/output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg')
Outliers were detected at volumes: [ 59. 102.]
