Hi Zhennan
there is an option to mri_ca_label to read in a prior segmentation and iterate the MRF minimization, but unless your labels and conventions are identical to our's it's unlikely to work. You can use mri_ca_train to build the MRF and likelihoods and such if you want.
cheers Bruce
On Wed, 30 Jan 2013, Zhennan Yan wrote:
Dear freesurfer experts,
I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). How can I do this using Freesurfer?
(2) If I have several subjects with labels, how can I train the anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my own program?
Many thanks!
Best, Zhennan