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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,106 @@ [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. -
Jan 28, 2019 .There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,62 @@ [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