Aligning BOLD data across sessions in functional output space

[Barbora]

Is there a way in fmriprep to align BOLD data from multiple runs and across sessions with the output being in func space (i.e. not registering to a standard or anatomical space?
Ideally, this process would involve multiple steps: 1. calculating the motion transforms within run using mcflirt and 2. use flirt to calculate the transform between each run’s boldref and a single template (let’s say from the very first run) and 3. reslicing in one step. Is anything like this possible in fmriprep?

[jsein]

Hi some attemps have been made, but nothing is ready out of the box in fmriprep right now:

Is it possible to specify a target EPI volume to realign to (motion correct to) in fmriprep?

Hi @12552 I’m struggling with some of the same issues that you describe here. Was curious if you had any success with any of the two approaches you suggested?

fMRIPrep coregistration within sessions?

For pepolar fieldmaps, the reference is actually the mean image estimated by TOPUP. In the future, I would like to select as the reference the EPI image that matches the polarity of the BOLD/SBREF file to be corrected, but this works well enough most of the time. Yes. I see, so if there were any issues, they would more likely be with co-registration of the 2nd session, rather than with SDC? Yes. A bad registration of a fieldmap to a BOLD volume would mean performing a warp where the expe…