Hi, where can I learn about how to deal with the following situation:
We are doing effectively 2 sessions in one visit. First using the 8-channel coil we collect a T1 and 6 EPIs for retinotopy data. Then the subject gets out, we switch to the 32-channel coil, and we collect another T1 and 2 longer resting-state EPIs.
We have to do this switch essentially because the 32-channel coil occludes too much of the display, but we need the 32-channel to use the desired resting-state sequence.
So #1 question is, can I preprocess all of this together somehow so that all the data is aligned at once? There are also fieldmaps that I think can be appended to the T1s in each session, does fmriprep know how to handle all this?
Or must I treat these as separate sessions and figure it out from there?
This sounds more like doing two different acquisitions in one session. Typically sessions happen across different days. An exception I guess would be if you are doing entire scanning protocols with the different coils, in which case it may make more sense to put the two coils in different session folders.
I don’t think you’d have to make any changes to fmriprep for it to work properly. It will align your BOLD images to the T1 as part of the functional workflow.
I’m not sure what you mean by append a fieldmap to a T1. These are separate files that should be in separate folders (T1 in anat, fieldmap in fmap). fMRIPrep currently has susceptibility distortion correction for BOLD data using the fieldmaps. To make the association between fmap and BOLD image, you need to add the IntendedFor field in the fmap jsons.