Bids-filter-file to select a single run - error json syntax error

Hello,

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

I would like 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
–md-only-boilerplate
–fs-license-file /storage/users/iliopoul/fs_license.txt
–fs-no-reconall
–output-spaces MNI152NLin2009cAsym:res-2
–verbose
–stop-on-first-crash
-t itemobject
–write-graph \

Anything you recognize as wrong here? How should I differenty use the bids file to select run 002?

Thank you a lot in advance :slight_smile:

Best,
Pan

Solved on BIDS error (code: 1 NOT INCLUDED; code: 63 - SESSION LLEGAL CHARACTER) - #4 by Steven (just replace ' with ")

MANAGED BY INCF