You will have to do it manually. You can create a binary CSF mask from the aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST" not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf). Then use mri_label2vol to map it into the functional space. Once there, mask the brain.nii.gz files (found in fsd/masks and fsd/RRR/masks where RRR is each run) using cp brain.nii.gz brain.orig.nii.gz fscalc yourmask.nii.gz not and brain.orig.nii.gz -o brain.nii.gz The rerun selxavg3-sess. It should automatically update from the brain mask point in the pipeline
On 10/8/2019 12:56 PM, stefano.silv...@libero.it<mailto:stefano.silv...@libero.it> wrote: 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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