[Freesurfer] Using own parcellation atlas

Hi experts,

I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions: - I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer? - Can I run this step in autorecon3 (step 28)? Or should I rerun recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)”

Thank you, Julie