[Freesurfer] brain mask without CSF ...

External Email - Use Caution

Dear FreeSurfer Experts,

I am running a functional analysis of subcortical structures using FS-FAST (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a brain mask excluding CSF; would it be possible using some option/flag in 'preproc-sess'?

or should I do it manually? maybe using a command like that?

mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o $sbjdir/mri/GM-WM_mask.mgz

because I saw in FreeSurferColorLUT.txt the following definitions:

702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0

or is there another strategy?

thanks in advance best stefano silvoni