I am currently in the middle of recording a multi-session MEG data set and want to store the data in a BIDS compatible way. So far, I used
mne_bids for the BIDS-conversion and things work quite nicely. However, now I also want to add the anatomical scan per subject to the data set I and I am not sure I understand the procedure to do it. Specifically, I wonder on which level would I include the anatomical scan? As there is only a single scan per subject, it doesn’t really make sense to put it on the modality level within every session, right? Would it be more appropriate to have a separate session, alike to the procedure with empty rooms?
In the BIDS-specs, I found following passage describing how to link anatomical scan to corresponding sessions in the json file, but can’t really wrap my head around what that implies for folder organization
Path or list of path relative to the subject subfolder pointing to the structural MRI, possibly of different types if a list is specified, to be used with the MEG recording. The path(s) need(s) to use forward slashes instead of backward slashes (for example,
Is there maybe an example data set online anywhere that I could use as template/inspiration. This one here comes close, but doesn’t really answer my questions.
Apart from that, I am also not certain on how to use mne-bids to add anatomical scans to the directory. If I am not mistaken, niftis (let alone dicoms) won’t do, I first need to myself get the surfaces from freesurfer, which can then be read out by mne_bids to produce all necessary files, including the transforms? Or do I need to compute the transforms and do the co-registration myself before invoking mne_bids? Only these files will then be included in the data set and not the “raw” nifti?
I appreciate any pointers/resources.