Hi, I am a student at NeuroPoly and we are converting our database for a project we are working on to a format compliant with the BIDS convention.
There are however a few scans for each subject in our database for which we are not sure what the correct filename should be so that it is BIDS-compliant. These are the filenames for these scans at the moment:
sub-SUBJ_acq-coilQaSagLarge_SNR.nii.gz
sub-SUBJ_acq-coilQaSagSmall_GFactor.nii.gz
sub-SUBJ_acq-coilQaTra_GFactor.nii.gz
sub-SUBJ_acq-famp_TB1DREAM.nii.gz
sub-SUBJ_acq-refv_TB1DREAM.nii.gz
For now, we have given them these placeholder suffixes: SNR, GFactor, TB1DREAM. These suffixes are however not valid BIDS suffixes.
What would be the correct suffixes for these files so that they can be BIDS compliant?
The discussion about the BIDS conversion of our database has so far been on GitHub, in this PR and in this issue.
Can you explain what these files are and how they were generated? If these files are not “raw” (I.e, direct from the scanner), then they may be more appropriate as a derivative, which in many cases do not have BIDS-standardized naming conventions. Depending on the kind of data, there may be a BIDS extension for it that lays out the naming convention. If not, you’re welcome to create your own BIDS extension proposal (BEP)!
An SNR image is definitely derivative, but if it’s coming off the scanner and valuable to include in your dataset, you can include it in a raw dataset; it just can’t be validated. I would look at BEP012 for how it is likely to become standard to do these, and then add them to a .bidsignore file. Please, when using .bidsignore, make sure you are using it in the spirit of Common principles - Unspecified data.
I have no idea what a GFactor map might be, but hopefully the above advice can guide you a bit. Feel free to ask follow-up questions.
For the SNR image, we’ll look into how to add them to a .bidsignore file.
For the DREAM scans: the scanner outputs a flip angle map (sub-SUBJ_acq-famp_TB1DREAM.nii.gz) and a reference voltage map (sub-SUBJ_acq-refv_TB1DREAM.nii.gz). The BIDS documentation specifies how to name flip angle and reference voltage maps for various other types of sequences (like TurboFLASH, “TB1TFL” and AFI, “TB1AFI”), however DREAM is not currently supported. Would the appropriate way to deal with these scans also be to include them in a .bidsignore file?
I’m afraid I don’t know enough about qMRI sequences to advise you better. @agahkarakuzu Are you at all familiar with DREAM, and can it be encoded under BIDS as-is?