BIDS Folder Structure - CPAC Output

I’m trying to figure out why my CPAC output folder may be rewriting subjects from the same institution. Here’s how my raw fMRI data is structured:







My CPAC output is structured as follows:



anat outputs


func outputs

To avoid overwriting subjects from the same institution, and to keep the subject ID in the folder structure, should I rename my raw folders? I.e, should sub-NYU_29240 be revised to sub-NYU29240?

Basically, I’m trying to keep track of subject IDs in my output folder (they are currently omitted, as you can see) and avoid overwriting subjects from the same institution. Thanks in advance.

Hello @asd_tms,

It seems this might be more of a general BIDS question - yes, in order to be compliant with BIDS, your subject IDs have to be within the same underscore demarcation. So, at the very least you should reformat your folder structure such that your raw data filenames begin with sub-NYU29240_*.nii.gz.

And if I’m not mistaken, ideally, each BIDS raw data folder should be dedicated to a single site, and the site name included in dataset_description.json at the root level, with the subject IDs as just sub-29240_*, etc. although I’m not sure if that’s a hard requirement. See the sample directory structure.

C-PAC, and most other neuroimaging software tools in the field, are designed to expect BIDS-compliant data directories, so reformatting your directory structure and file naming would be the easiest and most straightforward way to avoid any issues going forward.

Hope this helps.

Steve G.