I ran fMRIPrep including the FreeSurfer pipeline. For each subject, I want to convert annotations from the aparc parcellation (Desikan-Killiany atlas) to the T1w volume-space of the subject, to use as a ROI in MVPA (using cosmomvpa in matlab, with the GLM outputs from SPM12 based on the functional runs in T1w volume space). In doing this, I want to combine the Fusiform, Parahippocampal and Infero-Temporal areas of each hemisphere and then combine across hemispheres to have one ROI per subject. When converting the ROI to the volume space, it would be useful I think if the ROI covers the full grey matter without crossing over into the white matter.

I’m unsure of all the correct steps I need to take to achieve this and hoped that somebody could help me out with that. I want to make sure that everything is correctly registered for example. I’ve searched online, but could only find a couple of relevant tutorials that still leave me unsure of what to do exactly in my situation. Relevant tutorials: https://ggooo.wordpress.com/2014/10/12/extracting-a-volumetric-roi-from-an-annotation-file/ https://hippocampish.wordpress.com/2014/03/06/getting-cortical-rois-from-freesurfer/ https://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/

The steps I think I need to take for each subject, but not sure if correct (order) and not sure about the specifics either:

All help would greatly be appreciated!