Hello Freesurfers,

I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s. I want to use the ROIs for tractography, and therefore need them to include the underlying white matter.

I I am aware that freesurfer can do this after running the subjects through recon-all using freesurfer's own atlas. But is there a way to do this using the cortical ROIs defined in native space? So can I give freesurfer the T1 and the cortical ROIs as input and get the volumetric ROIs (that include white matter) as output in each subject's native space? This is important because the ROIs come from fMRI and are not based on the anatomy.

A detailed answer would be highly appreciated.

Many thanks,

Ahmad