Hello everybody,

I face some BIDS format problems when i try to run fmriprep (latest stable version) in a virtual linux machine.

I haven’t much experience from BIDS format, but to me it seems that ses-001, and subs are inside the folders as they should be.

I attach the errors, + data structure. Your wisdom can be valuable to finally solve this.

Thank you in advance :slight_smile:


  1. should just be README (you can remove the .md extension)
  2. is not a valid file. If you want to keep it in your bids directory, you can add the file name to a .bidsignore file in your BIDS root directory
  3. rev-enc is not a valid BIDS label. You can change it to acq-revenc or something along those lines.
  4. task_itemobject should be task-itemobject
  5. .mat files are not BIDS valid. events files should be .tsv files. I do not know what the numbers files are, but similar to if you want the validator to ignore the files, add these files to a .bidsignore file.
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Dear Steven,

Thanks again so much for your comment and help. Finally I managed to get my script running.

I struggle however to get the --bids-filter-file working.

I want to only process the fmri bold task run 002 and thus copied the json that fmriprep by default uses, by adding the ‘run’ field, see

{ 'fmap': {'datatype': 'fmap'},
  'bold': {'datatype': 'func', 'run': '002', 'suffix': 'bold'},
  'sbref': {'datatype': 'func', 'suffix': 'sbref'},
  'flair': {'datatype': 'anat', 'suffix': 'FLAIR'},
  't2w': {'datatype': 'anat', 'suffix': 'T2w'},
  't1w': {'datatype': 'anat', 'suffix': 'T1w'},
  'roi': {'datatype': 'anat', 'suffix': 'roi'} }

I get this error:
fmriprep: error: JSON syntax error in: </storage/users/iliopoul/PHD/data/MEMTRAIN2/bids_filter.json>.

I ran:
singularity --verbose run -B /storage/ /usr/local/bin/fmriprep-20.2.6.simg $bids_root_dir $out_dir/derivatives participant
–participant-label $subj
-w $workdir
–bids-filter-file /storage/users/iliopoul/PHD/data/MEMTRAIN2/bids_filter.json
–fs-license-file /storage/users/iliopoul/fs_license.txt
–output-spaces MNI152NLin2009cAsym:res-2
-t itemobject
–write-graph \

Anything you recognize as wrong here?


Hmmm, nothing immediately seems wrong with this, as all brackets are closed and there are no missing ' . Maybe try replacing all of the ' with "? Sometimes when you copy and paste ' they are encoded incorrectly. Does it look like words between the apostrophes are coded as strings?

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I saw that some others were using " " but didnt expect that to really affect sth. But it seems that it runs now! Thanks a lot you are the real mvp. :slight_smile:

Just a lucky guess on my part, happy it’s running now!

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