Unable to track IFOF with 5TT

[Antonin_Skoch]

I think that better than brain.mgz is to use norm.mgz, given the fact, that ’ the brain.mgz is very aggressively filtered explicitly for cortex and wipes away some subcortical boundaries (e.g. lateral thalamus) ’ - citation of this post in FreeSurfer forum:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51459.html

Therefore your accuracy of determination of subcortical gray matter is limited with brain.mgz.

Maybe, even better option would be to use brain.mgz for estimation of cortical GM, but use norm.mgz for estimation of subcortical GM.

Or, as I pointed out here:

FreeSurfer's mri_compute_volume_fractions as 5tt input to ACT

Dear experts, I was wondering if you have some experience with using FreeSurfer’s (FS) tool mri_compute_volume_fractions for generation of 5tt image for ACT. It seems that this tool produces much better GM/WM/CSF estimations than FAST. Especially the cortex boundary is better delineated and no subcortical structures and voxels adjacent to ventricles are assigned as cortical GM. The only issue is in the potential subcortical structures replacement by FIRST, since in mri_compute_volume_fractions …

maybe the best option for 5tt generation would be to use output of FreeSurfer’s mri_compute_volume_fractions.

Antonin