BIDS Compliance

Software Support
1

Hi everyone,

I am currently trying to convert my data into BIDS format using heudiconv (customized script) but upon running bids-validator I get the following error…does anyone have any idea what the problem might be? Possibly the acq label? Thanks for your help in advance!

 1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
                ./sub-1001/fmap/sub-1001_task-dwi_acq-dwi_dir-AP_epi.json
                        Evidence: sub-1001_task-dwi_acq-dwi_dir-AP_epi.json
                ./sub-1001/fmap/sub-1001_task-dwi_acq-dwi_dir-AP_epi.nii.gz
                        Evidence: sub-1001_task-dwi_acq-dwi_dir-AP_epi.nii.gz
                ./sub-1001/fmap/sub-1001_task-dwi_acq-dwi_dir-PA_epi.json
                        Evidence: sub-1001_task-dwi_acq-dwi_dir-PA_epi.json
                ./sub-1001/fmap/sub-1001_task-dwi_acq-dwi_dir-PA_epi.nii.gz
                        Evidence: sub-1001_task-dwi_acq-dwi_dir-PA_epi.nii.gz
                ./sub-1001/func/sub-1001_task-rest_run-01_acq-func_bold.json
                        Evidence: sub-1001_task-rest_run-01_acq-func_bold.json
                ./sub-1001/func/sub-1001_task-rest_run-01_acq-func_bold.nii.gz
                        Evidence: sub-1001_task-rest_run-01_acq-func_bold.nii.gz
                ./sub-1001/func/sub-1001_task-rest_run-01_acq-func_events.tsv
                        Evidence: sub-1001_task-rest_run-01_acq-func_events.tsv
                ./sub-1002/fmap/sub-1002_task-dwi_acq-dwi_dir-AP_epi.json
                        Evidence: sub-1002_task-dwi_acq-dwi_dir-AP_epi.json
                ./sub-1002/fmap/sub-1002_task-dwi_acq-dwi_dir-AP_epi.nii.gz
                        Evidence: sub-1002_task-dwi_acq-dwi_dir-AP_epi.nii.gz
                ./sub-1002/fmap/sub-1002_task-dwi_acq-dwi_dir-PA_epi.json
                        Evidence: sub-1002_task-dwi_acq-dwi_dir-PA_epi.json
                ... and 701 more files having this issue (Use --verbose to see them all).
2

Hi @neekee, and welcome to Neurostars!

You cannot have task-dwi (or any task-<> label) in fmap filenames.

The acq label must come before the run label.

For a full description of naming conventions, please see the specification here.

Best,
Steven

3

Hi Steven,

Thank you and thanks so much for your quick response! I’ll implement these changes and hopefully bids-validator won’t give me any more errors.

Best,
Nikki

1 Like
4

If you just need the filename templates for all modalities I am trying to now have all of them in single page in the bids starter kit:

https://bids-standard.github.io/bids-starter-kit/folders_and_files/files.html#modalities

Entities always follow the same sequence, though for some modalities some entities are not allowed.
If you want to know what is the order of all BIDS entities, see this appendix:

https://bids-specification.readthedocs.io/en/latest/appendices/entities.html

1 Like