Skip to content

Instantly share code, notes, and snippets.

Embed
What would you like to do?
fmriprep-1.2.6_fix with .nii.gz
[gillesd@tcn987 ~]$ singularity run fmriprep-1.2.6_fix.simg ~/fmriprep_sourcedata/ ~/derivatives/ participant --participant-label 02 --fs-license-file ~/license.txt
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.gz
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii.gz
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii.gz
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.gz
./sub-02/func/sub-02_task-randomdotmotion_run-02_bold.nii.gz
./sub-02/func/sub-02_task-randomdotmotion_run-03_bold.nii.gz
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, 39.9GB 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"""
190128-17:24:55,143 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.2.6-1:
* BIDS dataset path: /home/gillesd/fmriprep_sourcedata.
* Participant list: ['02'].
* Run identifier: 20190128-172455_0f9c0d7a-df3e-44c8-afa2-74e079224b52.
/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.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.