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January 28, 2019 15:08
Fmriprep 1.2.6 fails using singularity on cluster
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| [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 |
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| [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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