[Freesurfer] Skull stripping quality assessment

External Email - Use Caution Hello all, I want to assess the skull stripping quality performed in Freesurfer (autorecon1) and in FSL. Does any program enable to evaluate the skull stripping quality? If so, which metric is used for an evaluation? ___

Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

External Email - Use Caution Hi Doug, We thought it would be better to use 5th order icosahedron tesselation for PET because the resolution of the volume is lower: If, for thickness analysis, we carry the structural volumes with a resolution of 1x1x1 to ico7 on the surface, with P

[Freesurfer] Difference bewteen beta and ces in FS-FAST

External Email - Use Caution Dear FS experts, Hi!I have a very basic question about GLM model in FS-FAST.After GLM analysis, there is a beta.nii under the analysis/ directory and a ces.nii under each contrast/ directory. In the tutorial,  beta.nii is the regression coef

[Freesurfer] GLM DOSS question

External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients, aft

Re: [Freesurfer] Skull stripping quality assessment

Hi Adam the most common metric would involve doing a manual stripping, usually of a T2. Note that in FS we designed it using a risk-minimization approach that weighs removing brain as much more costly (~10x I think) then leaving around skull. cheers Bruce On Mon, 17 Feb 2020, Adam Rytina wr

[Freesurfer] Support with CVS/BBR Issue

External Email - Use Caution Dear FreeSurfer Community, I have used the CVS and BBR registration methods to spatially align T1 and diffusion images to an ideal subject’s T1. I have noticed some discrepancies when viewing the aligned images in FSLview. If I toggle between subjec