I am preprocessing structural data with FreeSurfer and I wonder if it is possible to use alternative parcellation atlas (e.g., Shen atlas, AAL) other than Desikan-Killiany or Destrieux which are given by default.
Same question to me. I wonder whether the anatomic subdivision atlas(e.g. AAL) is not commonly used in freesurfer. The atlas in freesurfer seems to be defined by the algorithm and focus on cortex, while AAL is an anatomical segmentation, dividing all the region in brain. Also, the AAL atlas is volumetric and how to convert it into a surf? As I know, the recon-all command is to deal with the brain file, not the atlas.