Hi Yang
mri_surf2surf will use the spherical registration to propagate the labels from one subject to another. mris_ca_label on the other hand will do a fully Bayesian segmentation using anisotropic non-stationary Markov Random Fields. In the end they probably aren’t hugely different as the folds are the dominant feature in each, but I would expect ca_label to be a bit better
cheers Bruce
From: Alex free_learner@foxmail.com Sent: Tuesday, July 14, 2026 10:00 PM To: freesurfer freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Differences between mri_surf2surf and mris_ca_label for cortical parcellation
External Email - Use Caution Dear experts,
As far as I know, there are two common ways to assign anatomical labels to cortical vertices: using mri_surf2surf (combined with an atlas annot file) and using mris_ca_label (which relies on a pre-trained classifier). My question is: in practice, which method is preferable?
Is mris_ca_label theoretically more accurate, but in reality the two yield nearly identical results? Or are there systematic, non-negligible differences? Also, is mris_ca_label less robust than the simpler projection method, particularly in subjects with imperfect surface reconstruction.
Thank you for your advice.
Yang Hu