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@Gilles86 Gilles86/fmriprep-1.2.6
Last active Jan 28, 2019

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Fmriprep 1.2.6 fails using singularity on cluster
[gillesd@tcn662 ~]$ singularity run fmriprep-1.2.6.simg ~/fmriprep_sourcedata/ ~/derivatives/ participant --participant-label 02 --fs-license-file ~/license.txt --output-space T1w
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [WARN] You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8 - EFFECTIVE_ECHO_SPACING_NOT_DEFINED)
./sub-02/func/sub-02_task-randomdotmotion_run-01_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii
2: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)
./sub-02/func/sub-02_task-randomdotmotion_run-01_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii
3: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)
./sub-02/anat/sub-02_T1w.nii
Summary: Available Tasks: Available Modalities:
100 Files, 41.27GB Random dot motion task with value-based biases T1w
14 - Subjects bold
1 - Session fieldmap
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)
190128-16:06:28,599 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.2.6:
* BIDS dataset path: /home/gillesd/fmriprep_sourcedata.
* Participant list: ['02'].
* Run identifier: 20190128-160628_1d14a068-9830-4b9f-b590-06ff3c1c03bd.
/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='/home/gillesd/fmriprep_sourcedata/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'))
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 740, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 217, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 383, in init_single_subject_wf
subject_data, layout = collect_data(bids_dir, subject_id, task_id, echo_idx)
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/utils/bids.py", line 181, in collect_data
subj_data.update({"bold": ses_uids})
UnboundLocalError: local variable 'ses_uids' referenced before assignment
[gillesd@tcn662 ~]$ singularity run fmriprep-1.2.6_fix.simg ~/fmriprep_sourcedata/ ~/derivatives/ participant --participant-label 02 --fs-license-file ~/license.txt --output-space T1w
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [WARN] You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8 - EFFECTIVE_ECHO_SPACING_NOT_DEFINED)
./sub-02/func/sub-02_task-randomdotmotion_run-01_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii
2: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)
./sub-02/func/sub-02_task-randomdotmotion_run-01_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii
3: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)
./sub-02/anat/sub-02_T1w.nii
Summary: Available Tasks: Available Modalities:
100 Files, 41.27GB Random dot motion task with value-based biases T1w
14 - Subjects bold
1 - Session fieldmap
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/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k
"""
/usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/cluster/supervised.py:578: DeprecationWarning: invalid escape sequence \s
"""
/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/utils.py:854: DeprecationWarning: invalid escape sequence \
'Rotation\ &\ Translation\ Matrix:\n(?P<rot_tran_mat>[0-9\.\ \n-]+)[\s\n]*'
/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/utils.py:863: DeprecationWarning: invalid escape sequence \.
'(?P<fwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*'
/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/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \#
"""
/usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:1429: DeprecationWarning: invalid escape sequence \c
"""
/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/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s
"""
/usr/local/miniconda/lib/python3.7/site-packages/sklearn/linear_model/omp.py:343: DeprecationWarning: invalid escape sequence \g
"""
/usr/local/miniconda/lib/python3.7/site-packages/svgutils/compose.py:347: DeprecationWarning: invalid escape sequence \.
m = re.match('([0-9]+\.?[0-9]*)([a-z]+)', measure)
/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/utils.py:214: DeprecationWarning: invalid escape sequence \d
pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+) '\
/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/_shared/_warnings.py:107: DeprecationWarning: invalid escape sequence \A
"""
/usr/local/miniconda/lib/python3.7/site-packages/skimage/restoration/deconvolution.py:118: DeprecationWarning: invalid escape sequence \h
"""
/usr/local/miniconda/lib/python3.7/site-packages/skimage/restoration/uft.py:23: DeprecationWarning: invalid escape sequence \s
"""
/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/skimage/measure/_regionprops.py:633: DeprecationWarning: invalid escape sequence \*
matches = re.finditer('\*\*(\w+)\*\* \:.*?\n(.*?)(?=\n [\*\S]+)',
/usr/local/miniconda/lib/python3.7/site-packages/skimage/transform/_geometric.py:530: DeprecationWarning: invalid escape sequence \m
"""
/usr/local/miniconda/lib/python3.7/site-packages/skimage/filters/rank/generic.py:49: DeprecationWarning: invalid escape sequence \-
"""
/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/fmap.py:501: DeprecationWarning: invalid escape sequence \D
"""Read :math:`\Delta_\text{TE}` from BIDS metadata dict"""
190128-16:06:47,729 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.2.6-1:
* BIDS dataset path: /home/gillesd/fmriprep_sourcedata.
* Participant list: ['02'].
* Run identifier: 20190128-160647_76876ec8-7639-4b39-87a7-fd9dfc9609e9.
/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/networkx/generators/geometric.py:275: DeprecationWarning: invalid escape sequence \l
"""
/usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/reciprocity.py:47: DeprecationWarning: invalid escape sequence \i
"""
/usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/shortest_paths/weighted.py:1996: DeprecationWarning: invalid escape sequence \p
"""
/usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/connectivity/connectivity.py:302: DeprecationWarning: invalid escape sequence \d
"""
/usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/line.py:113: DeprecationWarning: invalid escape sequence \{
"""
/usr/local/miniconda/lib/python3.7/site-packages/networkx/linalg/modularitymatrix.py:74: DeprecationWarning: invalid escape sequence \o
"""
/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/bids_layout.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/home/gillesd/fmriprep_sourcedata/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'))
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 749, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 217, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 389, in init_single_subject_wf
subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant 02 and task <all>. All workflows require BOLD images.
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