Fmriprep participant label not finding participant

Software Support
1

Summary of what happened:

Hello! I am trying to run the fmriprep sequence on singularity, and it is having trouble locating my files. My bids files are named as PILOT-P10_t1 etc… and it has trouble finding the files. I use the line below to locate my files.

Command used (and if a helper script was used, a link to the helper script or the command generated):

sbatch run_fmriprep.sh PILOT-P10

Version:

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity container

Data formatted according to a validatable standard? Please provide the output of the validator:

Unsure what this is

Relevant log outputs (up to 20 lines):

  File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 43, in main
    parse_args()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 812, in parse_args
    validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/utils/bids.py", line 175, in validate_input_dir
    raise RuntimeError(error_msg % ','.join(bad_labels))
RuntimeError: Data for requested participant(s) label(s) not found. Could not find data for participant(s): PILOT-P10. Please verify the requested participant labels. This error can be caused by the input data not being accessible inside the singularity container. Please make sure all paths are mapped properly (see https://www.sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html)

Screenshots / relevant information:

2

Hi @syoun,

Please do not delete the Software Support post template. You can see I edited it back in for you. Please fill out all the necessary information so we can assist you.

Best,
Steven

1 Like
3

Hi @syoun,

Please provide the full fmriprep command.

Also subject IDs should not have dashes (besides the sub-) or underscores in them. Sessions (e.g. t1) should be indicated in session folders, not in subject IDs.

The BIDS validation report should be among the first thing returned in the log. As long as you are not skipping bids validation.

Best,
Steven

4

Hello Steven,

I think I am indeed skipping the BIDS validation. However, after changing my file names to PILOT- etc to sub- etc resolved the issue! I did not know that would be the cause of it. Thank you very much.