Error when running fmriprep from singujlarity image

21

Remove the first \ after the .simg text.

22

Yes, I did it and now I got other warnings…

/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the config_filename, ignore, force_index, and index_metadata arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the indexer argument.
warnings.warn("The ability to pass arguments to BIDSLayout that control "
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main
parse_args()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 703, in parse_args
config.environment.exec_env, opts.bids_dir, opts.participant_label
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py”, line 145, 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): 003. 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)
rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol $

23

Is there a folder called sub-003 in /media/rosalia/Nuevo_vol/ARTICO/bids_dir? Have you run the bids-validator on /media/rosalia/Nuevo_vol/ARTICO/bids_dir to make sure it is BIDs compliant?

Best,
Steven

24

Hi Steven,

Thank you very much for your reply.
It is running, I moved sub-003 to bids_dir but it gave me two warnings:
1: [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-003/ses-BSL/func/sub-003_ses-BSL_task-rest_bold.nii

Please visit https://neurostars.org/search?q=SLICE_TIMING_NOT_DEFINED for existing conversations about this issue.

2: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
25

The warning is due to ‘SliceTiming’ not being defined in the associated .json file for the .nii, that is ./sub-003/ses-BSL/func/sub-003_ses-BSL_task-rest_bold.json, if such a file exists. How did you obtain these .niis? Using dcm2niix (especially recent versions) is good for producing BIDs-compliant JSON files. Slice timing correction isn’t necessary for fmri preprocessing (but usually recommended), so fMRIPrep should still proceed to completion.

BIDs datasets are supposed to have a README file describing the dataset. This should not impact fMRIPrep though.