fmriprep: singularity not executing despite using bids validated data

I just faced an issue similar to #1054 Ran the following singularity command: singularity run -B ./:$FS_LICENSE ${image} ./ ./output participant --participant-label=${participant}

Here’s what I get:

Process Process-2: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 383, in build_workflow bids_dir, participant_label=opts.participant_label) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/utils/bids.py", line 89, in collect_participants 'may need to adjust your "File sharing" preferences.', bids_dir) fmriprep.utils.bids.BIDSError: ---------- BIDS root folder: "/home/imawla" ---------- Could not find participants. Please make sure the BIDS data structure is present and correct. Datasets can be validated online using the BIDS Validator (http://incf.github.io/bids-validator/). If you are using Docker for Mac or Docker for Windows, you may need to adjust your "File sharing" preferences.

Here’s what the directory looks like:

 |-derivatives
 |-sub-CBTFM0001pre
 |---anat
 |---func
 |-sub-CBTFM0002pre
 |---anat
 |---func
 |-sub-CBTFM0003pre
 |---anat
 |---func
 |-sub-CBTFM0004pre
 |---anat
 |---func
 |-sub-CBTFM0005pre
 |---anat
 |---func

I am using version 1.0.15. BIDS validator was used to validate the directory, no issues there. Not sure what is happening, any help appreciated.

About this issue

  • Original URL
  • State: closed
  • Created 6 years ago
  • Comments: 19 (10 by maintainers)

Most upvoted comments

Hi, @effigies, Thanks for your response. I tried changing my code a few times and it worked finally. I guess it was some very subtle typo. sorry for my later reply.