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