In our lab, we have scanned a population of epilepsy patients. Some of the patients have had a brain resection. We are using fmriprep v23.2.1 to preprocess the fMRI data. For the patients with resections, can their BOLD series resampled to onto the cortical surfaces be included in a group analysis with the non-resection brains? My initial thought is no, because their cortical surfaces are missing brain structures such that the resectioned-brain vertices will not correspond to nonresectioned-brain vertices.
While it’s difficult to analyze a hemisphere that has been resectioned, you can still analyze the “good” hemisphere. Alignment to a template or standard processing pipelines like FreeSurfer’s recon-all may have difficulty with this kind of data though. For this kind of data, you can try lesion_align in AFNI which aligns good side or non-lesion brain to a half brain template. It also provides “healed” brains via mirroring and alignment-based methods that can then be used with FreeSurfer. The idea is that one would restrict analysis to the good side because resectioning removes anatomical landmarks.