Longitudinal Processing with sMRIPrep and QSIPrep

[jsein]

Hi @mkersey ,

When there are multiple sessions, the default for smriprep, qsiprep and fmriprep is to merge the anatomical image into what it is called a robust template, with the FreeSurfer methodology. There are different ways to merge several images into such a template. Here again, the default is to align this template on the first image (according to the name of the session in alphabetical order).
More details here.

If you want to process each session separately, you can follow the recommendation from @Steven from another thread:

What does fMRIPrep do with T1w with --longitudinal?

An alternative would be to use --bids-filter-file to specify to only use files from a certain session (which in your case may correspond to a longitudinal timepoint). Just note that you would not be able to reliably compare timepoints within subjects in subject space if you do this, since the T1s as you already pointed out will be appreciably different. Steven

For more details on the creation of the robust template within fmriprep (and also what happens to the T2w images), you can look at this other discussion:

Specify anatomic image

fMRIPrep will not merge T2w images. It will select one to pass to FreeSurfer, and that’s it. I believe the selection process is to take the highest resolution T2w image, and if multiple are found, the one that comes first in alphabetical order. It wouldn’t merge both together, though possibly I’m misreading. Could you share the listing of an anat/ directory?