fmriprep-unstable

gistfile1.txt

[gillesd@tcn600 ~]$ singularity run --cleanenv fmriprep-fix.simg /home/gillesd/fmriprep_sourcedata/ ~/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt --no-submm-recon
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-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
		./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
		./sub-01/func/sub-01_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-01/func/sub-01_task-randomdotmotion_run-01_bold.nii
		./sub-01/func/sub-01_task-randomdotmotion_run-02_bold.nii
		./sub-01/func/sub-01_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-01/anat/sub-01_T1w.nii

	4: [WARN] Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file. (code: 92 - MISSING_MAGNITUDE1_FILE)
		./sub-01/fmap/sub-01_phasediff.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/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)
190129-10:46:18,342 nipype.workflow IMPORTANT:

    Running fMRIPREP version 1.2.6-1+2.g6298bea5:
      * BIDS dataset path: /home/gillesd/fmriprep_sourcedata.
      * Participant list: ['01'].
      * Run identifier: 20190129-104618_f9415bef-d1fc-4419-934f-64881723ded8.

/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 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 01 and task <all>. All workflows require BOLD images.