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fmriprep-log-feb2019
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fmriprep-log-feb2019.txt
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.06.1-ce -v /Raid6/users/dan/Documents/licenses/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /Raid6/raw/midnight_scan_club:/data:ro -v /Raid6/raw/users/dan/Documents/Projects/midnight_test/data:/out -v /Raid6/users/dan/Documents/Projects/midnight_test/fmriprep_working_dir:/scratch poldracklab/fmriprep:1.2.6-1 /data /out participant --participant-label MSC01 --anat-only -w /scratch
WARNING: Error loading config file: /Raid6/users/dan/.docker/config.json: stat /Raid6/users/dan/.docker/config.json: permission denied
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
7717 Files, 108.71GB glasslexical bold
10 - Subjects memoryscenes T1w
14 - Sessions memorywords T2w
motor angio
rest fieldmap
memoryfaces
If you have any questions please post on https://neurostars.org/tags/bids
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-17:59:18,685 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.2.6-1:
* BIDS dataset path: /data.
* Participant list: ['MSC01'].
* Run identifier: 20190211-175918_9c7b7f14-d184-4b1f-a207-b170f386a7d3.
/usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping, Set, Iterable
/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/data/dataset_description.json' mode='r' encoding='UTF-8'>
self.description = json.load(open(target, 'r'))
/usr/local/miniconda/lib/python3.7/site-packages/grabbit/core.py:436: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/config/bids.json' mode='r' encoding='UTF-8'>
domain = json.load(open(domain, 'r'))
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-17:59:22,245 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the following boilerplate:
Results included in this manuscript come from preprocessing
performed using *fMRIPprep* 1.2.6-1
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.1.7
(@nipype1; @nipype2; RRID:SCR_002502).
Anatomical data preprocessing
: A total of 4 T1-weighted (T1w) images were found within the input
BIDS dataset.
All of them were corrected for intensity non-uniformity (INU)
using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0].
A T1w-reference map was computed after registration of
4 T1w images (after INU-correction) using
`mri_robust_template` [FreeSurfer 6.0.1, @fs_template].
The T1w-reference was then skull-stripped using `antsBrainExtraction.sh`
(ANTs 2.2.0), using OASIS as target template.
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Spatial normalization to the ICBM 152 Nonlinear Asymmetrical
template version 2009c [@mni, RRID:SCR_008796] was performed
through nonlinear registration with `antsRegistration`
[ANTs 2.2.0, RRID:SCR_004757, @ants], using
brain-extracted versions of both T1w volume and template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].
Many internal operations of *fMRIPrep* use
*Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
### References
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
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Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'DeprecationWarning'>): Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190211-17:59:30,212 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.bidssrc" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/bidssrc".
190211-17:59:30,216 nipype.workflow INFO:
[Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
190211-17:59:30,217 nipype.interface WARNING:
No "flair" images found for sub-<undefined>
190211-17:59:30,217 nipype.interface WARNING:
No "sbref" images found for sub-<undefined>
190211-17:59:30,217 nipype.interface WARNING:
No "roi" images found for sub-<undefined>
190211-17:59:30,228 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.bidssrc".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190211-17:59:33,655 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions".
190211-17:59:33,682 nipype.workflow INFO:
[Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
190211-17:59:33,766 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions".
190211-17:59:34,829 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name".
190211-17:59:34,830 nipype.workflow INFO:
[Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function")
190211-17:59:34,834 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190211-17:59:37,982 nipype.workflow INFO:
[Node] Setting-up "_t1_conform1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform1".
190211-17:59:37,984 nipype.workflow INFO:
[Node] Running "_t1_conform1" ("niworkflows.interfaces.images.Conform")
190211-17:59:37,985 nipype.workflow INFO:
[Node] Setting-up "_t1_conform2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2".
190211-17:59:37,985 nipype.workflow INFO:
[Node] Setting-up "_t1_conform0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0".
190211-17:59:37,987 nipype.workflow INFO:
[Node] Running "_t1_conform2" ("niworkflows.interfaces.images.Conform")
190211-17:59:37,987 nipype.workflow INFO:
[Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform")
190211-17:59:38,1 nipype.workflow INFO:
[Node] Setting-up "_t1_conform3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform3".
190211-17:59:38,2 nipype.workflow INFO:
[Node] Running "_t1_conform3" ("niworkflows.interfaces.images.Conform")
190211-17:59:38,68 nipype.workflow INFO:
[Node] Finished "_t1_conform1".
190211-17:59:38,68 nipype.workflow INFO:
[Node] Finished "_t1_conform0".
190211-17:59:38,70 nipype.workflow INFO:
[Node] Finished "_t1_conform3".
190211-17:59:38,75 nipype.workflow INFO:
[Node] Finished "_t1_conform2".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190211-17:59:41,655 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform".
190211-17:59:41,657 nipype.workflow INFO:
[Node] Setting-up "_t1_conform0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0".
190211-17:59:41,658 nipype.workflow INFO:
[Node] Cached "_t1_conform0" - collecting precomputed outputs
190211-17:59:41,658 nipype.workflow INFO:
[Node] "_t1_conform0" found cached.
190211-17:59:41,659 nipype.workflow INFO:
[Node] Setting-up "_t1_conform1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform1".
190211-17:59:41,660 nipype.workflow INFO:
[Node] Cached "_t1_conform1" - collecting precomputed outputs
190211-17:59:41,660 nipype.workflow INFO:
[Node] "_t1_conform1" found cached.
190211-17:59:41,660 nipype.workflow INFO:
[Node] Setting-up "_t1_conform2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2".
190211-17:59:41,661 nipype.workflow INFO:
[Node] Cached "_t1_conform2" - collecting precomputed outputs
190211-17:59:41,661 nipype.workflow INFO:
[Node] "_t1_conform2" found cached.
190211-17:59:41,662 nipype.workflow INFO:
[Node] Setting-up "_t1_conform3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform3".
190211-17:59:41,662 nipype.workflow INFO:
[Node] Cached "_t1_conform3" - collecting precomputed outputs
190211-17:59:41,662 nipype.workflow INFO:
[Node] "_t1_conform3" found cached.
190211-17:59:41,664 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_conform".
190211-17:59:45,194 nipype.workflow INFO:
[Node] Setting-up "_n4_correct0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0".
190211-17:59:45,196 nipype.workflow INFO:
[Node] Setting-up "_n4_correct3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3".
190211-17:59:45,196 nipype.workflow INFO:
[Node] Running "_n4_correct0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_T1w.nii.gz --output sub-MSC01_ses-struct01_run-01_T1w_corrected.nii.gz
190211-17:59:45,199 nipype.workflow INFO:
[Node] Running "_n4_correct3" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-02_T1w.nii.gz --output sub-MSC01_ses-struct02_run-02_T1w_corrected.nii.gz
190211-17:59:45,203 nipype.workflow INFO:
[Node] Setting-up "_n4_correct2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2".
190211-17:59:45,205 nipype.workflow INFO:
[Node] Setting-up "_n4_correct1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1".
190211-17:59:45,205 nipype.workflow INFO:
[Node] Running "_n4_correct2" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-01_T1w.nii.gz --output sub-MSC01_ses-struct02_run-01_T1w_corrected.nii.gz
190211-17:59:45,207 nipype.workflow INFO:
[Node] Running "_n4_correct1" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-02_T1w.nii.gz --output sub-MSC01_ses-struct01_run-02_T1w_corrected.nii.gz
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-17:59:46,494 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3".190211-17:59:46,494 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1".
190211-17:59:46,496 nipype.workflow INFO:
[Node] Running "_t1_conform_xfm3" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3/out.lta --src /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-02_T1w.nii.gz --trg /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-02_T1w.nii.gz190211-17:59:46,496 nipype.workflow INFO:
[Node] Running "_t1_conform_xfm1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1/out.lta --src /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-02_T1w.nii.gz --trg /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-02_T1w.nii.gz
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-17:59:46,501 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0".
190211-17:59:46,504 nipype.workflow INFO:
[Node] Running "_t1_conform_xfm0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0/out.lta --src /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_T1w.nii.gz --trg /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_T1w.nii.gz
190211-17:59:46,533 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2".
190211-17:59:46,535 nipype.workflow INFO:
[Node] Running "_t1_conform_xfm2" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2/out.lta --src /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-01_T1w.nii.gz --trg /data/sub-MSC01/ses-struct02/anat/sub-MSC01_ses-struct02_run-01_T1w.nii.gz
190211-17:59:46,620 nipype.workflow INFO:
[Node] Finished "_t1_conform_xfm3".
190211-17:59:46,638 nipype.workflow INFO:
[Node] Finished "_t1_conform_xfm1".
190211-17:59:46,652 nipype.workflow INFO:
[Node] Finished "_t1_conform_xfm0".
190211-17:59:46,654 nipype.workflow INFO:
[Node] Finished "_t1_conform_xfm2".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-17:59:49,932 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_conform_xfm" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm".
190211-17:59:49,935 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0".
190211-17:59:49,936 nipype.workflow INFO:
[Node] Cached "_t1_conform_xfm0" - collecting precomputed outputs
190211-17:59:49,936 nipype.workflow INFO:
[Node] "_t1_conform_xfm0" found cached.
190211-17:59:49,936 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1".
190211-17:59:49,937 nipype.workflow INFO:
[Node] Cached "_t1_conform_xfm1" - collecting precomputed outputs
190211-17:59:49,937 nipype.workflow INFO:
[Node] "_t1_conform_xfm1" found cached.
190211-17:59:49,938 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2".
190211-17:59:49,939 nipype.workflow INFO:
[Node] Cached "_t1_conform_xfm2" - collecting precomputed outputs
190211-17:59:49,939 nipype.workflow INFO:
[Node] "_t1_conform_xfm2" found cached.
190211-17:59:49,940 nipype.workflow INFO:
[Node] Setting-up "_t1_conform_xfm3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3".
190211-17:59:49,940 nipype.workflow INFO:
[Node] Cached "_t1_conform_xfm3" - collecting precomputed outputs
190211-17:59:49,940 nipype.workflow INFO:
[Node] "_t1_conform_xfm3" found cached.
190211-17:59:49,942 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_conform_xfm".
190211-18:03:39,406 nipype.workflow INFO:
[Node] Finished "_n4_correct3".
190211-18:03:40,375 nipype.workflow INFO:
[Node] Finished "_n4_correct2".
190211-18:04:05,286 nipype.workflow INFO:
[Node] Finished "_n4_correct0".
190211-18:04:05,532 nipype.workflow INFO:
[Node] Finished "_n4_correct1".
190211-18:04:07,26 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.n4_correct" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct".
190211-18:04:07,30 nipype.workflow INFO:
[Node] Setting-up "_n4_correct0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0".
190211-18:04:07,31 nipype.workflow INFO:
[Node] Cached "_n4_correct0" - collecting precomputed outputs
190211-18:04:07,31 nipype.workflow INFO:
[Node] "_n4_correct0" found cached.
190211-18:04:07,32 nipype.workflow INFO:
[Node] Setting-up "_n4_correct1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1".
190211-18:04:07,32 nipype.workflow INFO:
[Node] Cached "_n4_correct1" - collecting precomputed outputs
190211-18:04:07,32 nipype.workflow INFO:
[Node] "_n4_correct1" found cached.
190211-18:04:07,33 nipype.workflow INFO:
[Node] Setting-up "_n4_correct2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2".
190211-18:04:07,34 nipype.workflow INFO:
[Node] Cached "_n4_correct2" - collecting precomputed outputs
190211-18:04:07,34 nipype.workflow INFO:
[Node] "_n4_correct2" found cached.
190211-18:04:07,35 nipype.workflow INFO:
[Node] Setting-up "_n4_correct3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3".
190211-18:04:07,36 nipype.workflow INFO:
[Node] Cached "_n4_correct3" - collecting precomputed outputs
190211-18:04:07,36 nipype.workflow INFO:
[Node] "_n4_correct3" found cached.
190211-18:04:07,38 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.n4_correct".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:04:10,308 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_merge" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge".
190211-18:04:10,311 nipype.workflow INFO:
[Node] Running "t1_merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command:
mri_robust_template --satit --fixtp --mov /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-MSC01_ses-struct01_run-01_T1w_corrected.nii.gz /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-MSC01_ses-struct01_run-02_T1w_corrected.nii.gz /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-MSC01_ses-struct02_run-01_T1w_corrected.nii.gz /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-MSC01_ses-struct02_run-02_T1w_corrected.nii.gz --inittp 1 --iscale --noit --template sub-MSC01_ses-struct01_run-01_T1w_template.nii.gz --subsample 200 --lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta
190211-18:05:48,161 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_merge".
190211-18:05:49,53 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_reorient" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_reorient".
190211-18:05:49,55 nipype.workflow INFO:
[Node] Running "t1_reorient" ("nipype.interfaces.image.Reorient")
190211-18:05:49,180 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.t1_reorient".
190211-18:05:51,497 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip".
190211-18:05:51,500 nipype.workflow INFO:
[Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command:
antsBrainExtraction.sh -a /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/sub-MSC01_ses-struct01_run-01_T1w_template.nii.gz -m /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/tpl-OASIS30ANTs_res-01_class-brainmask_probtissue.nii.gz -e /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz -d 3 -f /templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BrainCerebellumExtraction_roi.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:05:52,903 nipype.workflow INFO:
[Node] Setting-up "_concat_affines3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines3".
190211-18:05:52,906 nipype.workflow INFO:
[Node] Running "_concat_affines3" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta -invertout -out_type 1 /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3/out.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta out_concat.lta
190211-18:05:52,908 nipype.workflow INFO:
[Node] Setting-up "_concat_affines1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines1".
190211-18:05:52,910 nipype.workflow INFO:
[Node] Running "_concat_affines1" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta -invertout -out_type 1 /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1/out.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta out_concat.lta
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:05:52,921 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/recon_config".
190211-18:05:52,922 nipype.workflow INFO:
[Node] Setting-up "_concat_affines2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines2".
190211-18:05:52,924 nipype.workflow INFO:
[Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
190211-18:05:52,925 nipype.workflow INFO:
[Node] Running "_concat_affines2" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta -invertout -out_type 1 /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2/out.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta out_concat.lta
190211-18:05:52,954 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.recon_config".
190211-18:05:52,968 nipype.workflow INFO:
[Node] Setting-up "_concat_affines0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines0".
190211-18:05:52,970 nipype.workflow INFO:
[Node] Running "_concat_affines0" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta -invertout -out_type 1 /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0/out.lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta out_concat.lta
190211-18:05:53,31 nipype.workflow INFO:
[Node] Finished "_concat_affines1".
190211-18:05:53,49 nipype.workflow INFO:
[Node] Finished "_concat_affines3".
190211-18:05:53,52 nipype.workflow INFO:
[Node] Finished "_concat_affines2".
190211-18:05:53,85 nipype.workflow INFO:
[Node] Finished "_concat_affines0".
190211-18:05:55,246 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
190211-18:05:55,249 nipype.workflow INFO:
[Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -i /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/sub-MSC01_ses-struct01_run-01_T1w_template.nii.gz -T2 /data/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_T2w.nii.gz -noskullstrip -hires -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -expert /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:05:56,484 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.concat_affines" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines".
190211-18:05:56,487 nipype.workflow INFO:
[Node] Setting-up "_concat_affines0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines0".
190211-18:05:56,488 nipype.workflow INFO:
[Node] Cached "_concat_affines0" - collecting precomputed outputs
190211-18:05:56,488 nipype.workflow INFO:
[Node] "_concat_affines0" found cached.
190211-18:05:56,489 nipype.workflow INFO:
[Node] Setting-up "_concat_affines1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines1".
190211-18:05:56,490 nipype.workflow INFO:
[Node] Cached "_concat_affines1" - collecting precomputed outputs
190211-18:05:56,490 nipype.workflow INFO:
[Node] "_concat_affines1" found cached.
190211-18:05:56,491 nipype.workflow INFO:
[Node] Setting-up "_concat_affines2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines2".
190211-18:05:56,491 nipype.workflow INFO:
[Node] Cached "_concat_affines2" - collecting precomputed outputs
190211-18:05:56,491 nipype.workflow INFO:
[Node] "_concat_affines2" found cached.
190211-18:05:56,492 nipype.workflow INFO:
[Node] Setting-up "_concat_affines3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines3".
190211-18:05:56,493 nipype.workflow INFO:
[Node] Cached "_concat_affines3" - collecting precomputed outputs
190211-18:05:56,493 nipype.workflow INFO:
[Node] "_concat_affines3" found cached.
190211-18:05:56,495 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.concat_affines".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:06:02,544 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk1".
190211-18:06:02,546 nipype.workflow INFO:
[Node] Running "_lta_to_itk1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines1/out_concat.lta --outitk /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk1/out.txt
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:06:02,580 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk0".
190211-18:06:02,582 nipype.workflow INFO:
[Node] Running "_lta_to_itk0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines0/out_concat.lta --outitk /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk0/out.txt
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:06:02,602 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk3".
190211-18:06:02,604 nipype.workflow INFO:
[Node] Running "_lta_to_itk3" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines3/out_concat.lta --outitk /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk3/out.txt
190211-18:06:02,625 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk2".
190211-18:06:02,628 nipype.workflow INFO:
[Node] Running "_lta_to_itk2" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/concat_affines/mapflow/_concat_affines2/out_concat.lta --outitk /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk2/out.txt
190211-18:06:02,678 nipype.workflow INFO:
[Node] Finished "_lta_to_itk1".
190211-18:06:02,709 nipype.workflow INFO:
[Node] Finished "_lta_to_itk0".
190211-18:06:02,731 nipype.workflow INFO:
[Node] Finished "_lta_to_itk3".
190211-18:06:02,737 nipype.workflow INFO:
[Node] Finished "_lta_to_itk2".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:06:06,248 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.lta_to_itk" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk".
190211-18:06:06,251 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk0".
190211-18:06:06,252 nipype.workflow INFO:
[Node] Cached "_lta_to_itk0" - collecting precomputed outputs
190211-18:06:06,252 nipype.workflow INFO:
[Node] "_lta_to_itk0" found cached.
190211-18:06:06,253 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk1".
190211-18:06:06,254 nipype.workflow INFO:
[Node] Cached "_lta_to_itk1" - collecting precomputed outputs
190211-18:06:06,254 nipype.workflow INFO:
[Node] "_lta_to_itk1" found cached.
190211-18:06:06,255 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk2".
190211-18:06:06,255 nipype.workflow INFO:
[Node] Cached "_lta_to_itk2" - collecting precomputed outputs
190211-18:06:06,255 nipype.workflow INFO:
[Node] "_lta_to_itk2" found cached.
190211-18:06:06,256 nipype.workflow INFO:
[Node] Setting-up "_lta_to_itk3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/lta_to_itk/mapflow/_lta_to_itk3".
190211-18:06:06,257 nipype.workflow INFO:
[Node] Cached "_lta_to_itk3" - collecting precomputed outputs
190211-18:06:06,257 nipype.workflow INFO:
[Node] "_lta_to_itk3" found cached.
190211-18:06:06,259 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_template_wf.lta_to_itk".
190211-18:11:59,677 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:12:02,707 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm".
190211-18:12:02,710 nipype.workflow INFO:
[Node] Running "fsnative_2_t1_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /out/freesurfer/sub-MSC01/mri/T1.mgz --dst /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_template_wf/t1_merge/sub-MSC01_ses-struct01_run-01_T1w_template.nii.gz
190211-18:13:18,538 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:13:20,669 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm".
190211-18:13:20,671 nipype.workflow INFO:
[Node] Running "t1_2_fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta
190211-18:13:20,777 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:13:24,668 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk".
190211-18:13:24,670 nipype.workflow INFO:
[Node] Running "lta_2_itk" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt
190211-18:13:24,762 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk".
190211-18:26:42,902 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190211-18:26:45,523 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
190211-18:26:45,525 nipype.workflow INFO:
[Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
190211-18:26:47,78 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
190211-18:26:48,400 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
190211-18:26:48,402 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-18:26:48,402 nipype.workflow INFO:
[Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-18:26:48,404 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:44,724 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
190211-21:15:48,281 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
190211-21:15:48,283 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
190211-21:15:48,284 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:48,284 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:48,286 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:48,287 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:48,287 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-21:15:48,289 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer
190211-23:13:59,667 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
190211-23:16:03,38 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
190211-23:16:05,70 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
190211-23:16:05,75 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
190211-23:16:05,78 nipype.interface INFO:
recon-all complete : Not running
190211-23:16:05,78 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
190211-23:16:05,80 nipype.interface INFO:
recon-all complete : Not running
190211-23:16:05,125 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
190211-23:16:05,130 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
190211-23:16:05,137 nipype.interface INFO:
recon-all complete : Not running
190211-23:16:05,138 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
190211-23:16:05,141 nipype.interface INFO:
recon-all complete : Not running
190211-23:16:05,196 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
190211-23:16:05,200 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
190211-23:16:09,156 nipype.workflow INFO:
[Node] Setting-up "_autorecon30" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30".
190211-23:16:09,159 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -hemi lh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190211-23:16:09,159 nipype.workflow INFO:
[Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -hemi lh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190211-23:16:09,161 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -hemi lh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190211-23:16:09,169 nipype.workflow INFO:
[Node] Setting-up "_autorecon31" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31".
190211-23:16:09,172 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -hemi rh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190211-23:16:09,173 nipype.workflow INFO:
[Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -hemi rh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190211-23:16:09,175 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -hemi rh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
190212-01:16:16,97 nipype.workflow INFO:
[Node] Finished "_autorecon31".
190212-01:21:01,390 nipype.workflow INFO:
[Node] Finished "_autorecon30".
190212-01:21:02,541 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
190212-01:21:02,545 nipype.workflow INFO:
[Node] Setting-up "_autorecon30" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30".
190212-01:21:02,548 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:02,548 nipype.workflow INFO:
[Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
190212-01:21:02,550 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:02,588 nipype.workflow INFO:
[Node] Finished "_autorecon30".
190212-01:21:02,591 nipype.workflow INFO:
[Node] Setting-up "_autorecon31" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31".
190212-01:21:02,594 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:02,594 nipype.workflow INFO:
[Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
190212-01:21:02,596 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:02,629 nipype.workflow INFO:
[Node] Finished "_autorecon31".
190212-01:21:02,632 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3".
190212-01:21:04,665 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces".
190212-01:21:04,666 nipype.workflow INFO:
[Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource")
190212-01:21:04,683 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces".
190212-01:21:04,697 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource".
190212-01:21:04,699 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
190212-01:21:04,714 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
190212-01:21:04,715 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
190212-01:21:04,721 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource".
190212-01:21:04,732 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190212-01:21:05,661 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/recon_report".
190212-01:21:05,664 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:05,664 nipype.workflow INFO:
[Node] Running "recon_report" ("niworkflows.interfaces.segmentation.ReconAllRPT"), a CommandLine Interface with command:
echo recon-all: nothing to do
190212-01:21:05,667 nipype.interface INFO:
recon-all complete : Not running
190212-01:21:06,568 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative".
190212-01:21:06,571 nipype.workflow INFO:
[Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command:
mri_label2vol --regheader /out/freesurfer/sub-MSC01/mri/aseg.mgz --seg /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg.mgz --temp /out/freesurfer/sub-MSC01/mri/rawavg.mgz --o /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz
190212-01:21:06,609 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative".
190212-01:21:06,611 nipype.workflow INFO:
[Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command:
mri_label2vol --regheader /out/freesurfer/sub-MSC01/mri/aseg.mgz --seg /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz --temp /out/freesurfer/sub-MSC01/mri/rawavg.mgz --o /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
return list(data) if isinstance(data, collections.MappingView) else data
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190212-01:21:09,722 nipype.workflow INFO:
[Node] Setting-up "_midthickness1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
190212-01:21:09,725 nipype.workflow INFO:
[Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.pial -thickness -thickness_name /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.thickness /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.smoothwm 0.5 midthickness
190212-01:21:09,747 nipype.workflow INFO:
[Node] Setting-up "_midthickness0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
190212-01:21:09,750 nipype.workflow INFO:
[Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial -thickness -thickness_name /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.smoothwm 0.5 midthickness
190212-01:21:13,741 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report".
190212-01:21:14,9 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative".
190212-01:21:14,392 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative".
190212-01:21:16,624 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii".
190212-01:21:16,628 nipype.workflow INFO:
[Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --out_type nii --resample_type nearest --reslice_like /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz --input_volume /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz --output_volume /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz
190212-01:21:16,665 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii".
190212-01:21:16,669 nipype.workflow INFO:
[Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --out_type nii --resample_type nearest --reslice_like /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz --input_volume /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz --output_volume /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz
190212-01:21:19,350 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii".
190212-01:21:19,532 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190212-01:21:21,827 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.refine" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/refine".
190212-01:21:21,991 nipype.workflow INFO:
[Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask")
190212-01:22:27,243 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.refine".
190212-01:22:27,959 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.applyrefined" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/applyrefined".
190212-01:22:27,963 nipype.workflow INFO:
[Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz -mas /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/refine/highres001_N4Corrected0_rbrainmask.nii.gz /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/applyrefined/highres001_N4Corrected0_masked.nii.gz
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190212-01:22:29,481 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.t1_2_mni" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni".
190212-01:22:29,482 nipype.workflow INFO:
[Node] Running "t1_2_mni" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT")
190212-01:22:29,886 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.applyrefined".
190212-01:22:31,878 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.t1_seg" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg".
190212-01:22:31,884 nipype.workflow INFO:
[Node] Running "t1_seg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -N -p -g -S 1 /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg/highres001_N4Corrected0_masked.nii.gz
190212-01:26:13,31 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.t1_seg".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190212-01:26:15,355 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.seg_rpt" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/seg_rpt".
190212-01:26:15,356 nipype.workflow INFO:
[Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot")
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
return list(data) if isinstance(data, collections.MappingView) else data
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32
warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux))
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
/usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index
return _nd_image.find_objects(input, max_label)
190212-01:27:24,242 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.seg_rpt".
190212-01:47:19,876 nipype.workflow INFO:
[Node] Finished "_midthickness1".
190212-01:48:21,676 nipype.workflow INFO:
[Node] Finished "_midthickness0".
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190212-01:48:23,647 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness".
190212-01:48:23,650 nipype.workflow INFO:
[Node] Setting-up "_midthickness0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
190212-01:48:23,651 nipype.workflow INFO:
[Node] Cached "_midthickness0" - collecting precomputed outputs
190212-01:48:23,651 nipype.workflow INFO:
[Node] "_midthickness0" found cached.
190212-01:48:23,652 nipype.workflow INFO:
[Node] Setting-up "_midthickness1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
190212-01:48:23,653 nipype.workflow INFO:
[Node] Cached "_midthickness1" - collecting precomputed outputs
190212-01:48:23,653 nipype.workflow INFO:
[Node] "_midthickness1" found cached.
190212-01:48:23,654 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness".
190212-01:48:25,429 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness".
190212-01:48:25,434 nipype.workflow INFO:
[Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
190212-01:48:25,544 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
190212-01:48:31,424 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0".
190212-01:48:31,426 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1".
190212-01:48:31,427 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2".
190212-01:48:31,428 nipype.workflow INFO:
[Node] Running "_fs_2_gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/lh.smoothwm /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0/lh.smoothwm_converted.gii
190212-01:48:31,429 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3".
190212-01:48:31,429 nipype.workflow INFO:
[Node] Running "_fs_2_gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/rh.pial /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2/rh.pial_converted.gii
190212-01:48:31,430 nipype.workflow INFO:
[Node] Running "_fs_2_gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/rh.smoothwm /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/rh.smoothwm_converted.gii
190212-01:48:31,431 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii4" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4".
190212-01:48:31,432 nipype.workflow INFO:
[Node] Running "_fs_2_gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/lh.pial /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/lh.pial_converted.gii
190212-01:48:31,433 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii5" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5".
190212-01:48:31,434 nipype.workflow INFO:
[Node] Running "_fs_2_gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/lh.inflated /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii
190212-01:48:31,435 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii6" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6".
190212-01:48:31,435 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii7" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7".
190212-01:48:31,436 nipype.workflow INFO:
[Node] Running "_fs_2_gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/rh.inflated /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5/rh.inflated_converted.gii
190212-01:48:31,438 nipype.workflow INFO:
[Node] Running "_fs_2_gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/rh.midthickness /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7/rh.midthickness_converted.gii
190212-01:48:31,439 nipype.workflow INFO:
[Node] Running "_fs_2_gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-MSC01/surf/lh.midthickness /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/lh.midthickness_converted.gii
190212-01:48:34,302 nipype.workflow INFO:
[Node] Finished "_fs_2_gii0".
190212-01:48:34,309 nipype.workflow INFO:
[Node] Finished "_fs_2_gii3".
190212-01:48:34,314 nipype.workflow INFO:
[Node] Finished "_fs_2_gii2".
190212-01:48:34,318 nipype.workflow INFO:
[Node] Finished "_fs_2_gii4".
190212-01:48:34,322 nipype.workflow INFO:
[Node] Finished "_fs_2_gii7".
190212-01:48:34,351 nipype.workflow INFO:
[Node] Finished "_fs_2_gii5".
190212-01:48:34,391 nipype.workflow INFO:
[Node] Finished "_fs_2_gii6".
190212-01:48:34,623 nipype.workflow INFO:
[Node] Finished "_fs_2_gii1".
190212-01:48:35,498 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii".
190212-01:48:35,502 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0".
190212-01:48:35,502 nipype.workflow INFO:
[Node] Cached "_fs_2_gii0" - collecting precomputed outputs
190212-01:48:35,503 nipype.workflow INFO:
[Node] "_fs_2_gii0" found cached.
190212-01:48:35,503 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1".
190212-01:48:35,504 nipype.workflow INFO:
[Node] Cached "_fs_2_gii1" - collecting precomputed outputs
190212-01:48:35,504 nipype.workflow INFO:
[Node] "_fs_2_gii1" found cached.
190212-01:48:35,505 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2".
190212-01:48:35,506 nipype.workflow INFO:
[Node] Cached "_fs_2_gii2" - collecting precomputed outputs
190212-01:48:35,506 nipype.workflow INFO:
[Node] "_fs_2_gii2" found cached.
190212-01:48:35,507 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3".
190212-01:48:35,508 nipype.workflow INFO:
[Node] Cached "_fs_2_gii3" - collecting precomputed outputs
190212-01:48:35,508 nipype.workflow INFO:
[Node] "_fs_2_gii3" found cached.
190212-01:48:35,509 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii4" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4".
190212-01:48:35,509 nipype.workflow INFO:
[Node] Cached "_fs_2_gii4" - collecting precomputed outputs
190212-01:48:35,509 nipype.workflow INFO:
[Node] "_fs_2_gii4" found cached.
190212-01:48:35,510 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii5" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5".
190212-01:48:35,511 nipype.workflow INFO:
[Node] Cached "_fs_2_gii5" - collecting precomputed outputs
190212-01:48:35,511 nipype.workflow INFO:
[Node] "_fs_2_gii5" found cached.
190212-01:48:35,512 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii6" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6".
190212-01:48:35,513 nipype.workflow INFO:
[Node] Cached "_fs_2_gii6" - collecting precomputed outputs
190212-01:48:35,513 nipype.workflow INFO:
[Node] "_fs_2_gii6" found cached.
190212-01:48:35,514 nipype.workflow INFO:
[Node] Setting-up "_fs_2_gii7" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7".
190212-01:48:35,514 nipype.workflow INFO:
[Node] Cached "_fs_2_gii7" - collecting precomputed outputs
190212-01:48:35,515 nipype.workflow INFO:
[Node] "_fs_2_gii7" found cached.
190212-01:48:35,518 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii".
190212-01:48:39,445 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs4" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
190212-01:48:39,446 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs6" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
190212-01:48:39,447 nipype.workflow INFO:
[Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf")190212-01:48:39,447 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs7" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
190212-01:48:39,447 nipype.workflow INFO:
[Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf")
190212-01:48:39,449 nipype.workflow INFO:
[Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf")
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7/rh.midthickness_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/lh.midthickness_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4/lh.inflated_converted.gii'>
self.to_file_map()
190212-01:48:40,161 nipype.workflow INFO:
[Node] Finished "_fix_surfs4".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6/lh.midthickness_converted.gii'>
self.to_file_map()
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
190212-01:48:40,209 nipype.workflow INFO:
[Node] Finished "_fix_surfs6".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7/rh.midthickness_converted.gii'>
self.to_file_map()
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190212-01:48:40,233 nipype.workflow INFO:
[Node] Finished "_fix_surfs7".
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190212-01:48:40,453 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
190212-01:48:40,454 nipype.workflow INFO:
[Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf")
190212-01:48:40,473 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
190212-01:48:40,475 nipype.workflow INFO:
[Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf")
190212-01:48:40,479 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
190212-01:48:40,480 nipype.workflow INFO:
[Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf")
190212-01:48:40,487 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs5" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
190212-01:48:40,489 nipype.workflow INFO:
[Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf")
190212-01:48:40,497 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
190212-01:48:40,498 nipype.workflow INFO:
[Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf")
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2/rh.pial_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/rh.smoothwm_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0/lh.smoothwm_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/lh.pial_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5/rh.inflated_converted.gii'>
parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5/rh.inflated_converted.gii'>
self.to_file_map()
190212-01:48:41,195 nipype.workflow INFO:
[Node] Finished "_fix_surfs5".
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0/lh.smoothwm_converted.gii'>
self.to_file_map()
190212-01:48:41,254 nipype.workflow INFO:
[Node] Finished "_fix_surfs0".
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1/rh.smoothwm_converted.gii'>
self.to_file_map()
190212-01:48:41,279 nipype.workflow INFO:
[Node] Finished "_fix_surfs1".
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2/rh.pial_converted.gii'>
self.to_file_map()
190212-01:48:41,309 nipype.workflow INFO:
[Node] Finished "_fix_surfs2".
/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3/lh.pial_converted.gii'>
self.to_file_map()
190212-01:48:41,364 nipype.workflow INFO:
[Node] Finished "_fix_surfs3".
190212-01:48:43,435 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs".
190212-01:48:43,440 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
190212-01:48:43,442 nipype.workflow INFO:
[Node] Cached "_fix_surfs0" - collecting precomputed outputs
190212-01:48:43,442 nipype.workflow INFO:
[Node] "_fix_surfs0" found cached.
190212-01:48:43,443 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
190212-01:48:43,444 nipype.workflow INFO:
[Node] Cached "_fix_surfs1" - collecting precomputed outputs
190212-01:48:43,444 nipype.workflow INFO:
[Node] "_fix_surfs1" found cached.
190212-01:48:43,445 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
190212-01:48:43,445 nipype.workflow INFO:
[Node] Cached "_fix_surfs2" - collecting precomputed outputs
190212-01:48:43,445 nipype.workflow INFO:
[Node] "_fix_surfs2" found cached.
190212-01:48:43,446 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs3" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
190212-01:48:43,448 nipype.workflow INFO:
[Node] Cached "_fix_surfs3" - collecting precomputed outputs
190212-01:48:43,448 nipype.workflow INFO:
[Node] "_fix_surfs3" found cached.
190212-01:48:43,449 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs4" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
190212-01:48:43,451 nipype.workflow INFO:
[Node] Cached "_fix_surfs4" - collecting precomputed outputs
190212-01:48:43,451 nipype.workflow INFO:
[Node] "_fix_surfs4" found cached.
190212-01:48:43,452 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs5" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
190212-01:48:43,453 nipype.workflow INFO:
[Node] Cached "_fix_surfs5" - collecting precomputed outputs
190212-01:48:43,454 nipype.workflow INFO:
[Node] "_fix_surfs5" found cached.
190212-01:48:43,455 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs6" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
190212-01:48:43,456 nipype.workflow INFO:
[Node] Cached "_fix_surfs6" - collecting precomputed outputs
190212-01:48:43,456 nipype.workflow INFO:
[Node] "_fix_surfs6" found cached.
190212-01:48:43,456 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs7" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
190212-01:48:43,457 nipype.workflow INFO:
[Node] Cached "_fix_surfs7" - collecting precomputed outputs
190212-01:48:43,457 nipype.workflow INFO:
[Node] "_fix_surfs7" found cached.
190212-01:48:43,460 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs".
/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
return list(data) if isinstance(data, collections.MappingView) else data
190212-01:57:10,460 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.t1_2_mni".
190212-01:57:12,693 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_mask" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_mask".
190212-01:57:12,697 nipype.workflow INFO:
[Node] Running "mni_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/refine/highres001_N4Corrected0_rbrainmask.nii.gz --interpolation MultiLabel --output highres001_N4Corrected0_rbrainmask_trans.nii.gz --reference-image /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5
190212-01:57:12,700 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_seg" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_seg".
190212-01:57:12,704 nipype.workflow INFO:
[Node] Running "mni_seg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg/highres001_N4Corrected0_masked_seg.nii.gz --interpolation MultiLabel --output highres001_N4Corrected0_masked_seg_trans.nii.gz --reference-image /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5
190212-01:57:13,939 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0".
190212-01:57:13,941 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1".
190212-01:57:13,943 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2".
190212-01:57:13,983 nipype.workflow INFO:
[Node] Running "_mni_tpms0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg/highres001_N4Corrected0_masked_prob_0.nii.gz --interpolation Linear --output highres001_N4Corrected0_masked_prob_0_trans.nii.gz --reference-image /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5
190212-01:57:13,983 nipype.workflow INFO:
[Node] Running "_mni_tpms1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg/highres001_N4Corrected0_masked_prob_1.nii.gz --interpolation Linear --output highres001_N4Corrected0_masked_prob_1_trans.nii.gz --reference-image /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5
190212-01:57:13,983 nipype.workflow INFO:
[Node] Running "_mni_tpms2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_seg/highres001_N4Corrected0_masked_prob_2.nii.gz --interpolation Linear --output highres001_N4Corrected0_masked_prob_2_trans.nii.gz --reference-image /templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5
190212-01:57:17,343 nipype.workflow INFO:
[Node] Finished "_mni_tpms0".
190212-01:57:17,488 nipype.workflow INFO:
[Node] Finished "_mni_tpms1".
190212-01:57:17,540 nipype.workflow INFO:
[Node] Finished "_mni_tpms2".
190212-01:57:17,978 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_tpms" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms".
190212-01:57:17,984 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms0" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0".
190212-01:57:17,986 nipype.workflow INFO:
[Node] Cached "_mni_tpms0" - collecting precomputed outputs
190212-01:57:17,987 nipype.workflow INFO:
[Node] "_mni_tpms0" found cached.
190212-01:57:17,989 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms1" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1".
190212-01:57:17,991 nipype.workflow INFO:
[Node] Cached "_mni_tpms1" - collecting precomputed outputs
190212-01:57:17,991 nipype.workflow INFO:
[Node] "_mni_tpms1" found cached.
190212-01:57:17,992 nipype.workflow INFO:
[Node] Setting-up "_mni_tpms2" in "/scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2".
190212-01:57:17,993 nipype.workflow INFO:
[Node] Cached "_mni_tpms2" - collecting precomputed outputs
190212-01:57:17,993 nipype.workflow INFO:
[Node] "_mni_tpms2" found cached.
190212-01:57:17,994 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_tpms".
190212-01:59:42,548 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_mask".
190212-02:00:00,898 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_MSC01_wf.anat_preproc_wf.mni_seg".
Sentry is attempting to send 1 pending error messages
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Captured warning (<class 'ResourceWarning'>): unclosed <socket.socket fd=5, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6, laddr=('172.17.0.3', 34895), raddr=('35.188.42.15', 443)
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