Hi Fs Experts,

In order to calculate the global white matter fractional anisotropy FA I used  (wm.mgz ) the output of recon-all as a mask in the following command line

mri_segstats --seg $SUBJECTS_DIR/015601/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt  --mask wm.mgz  --i fa.anat.mgh  --sum fa.stats

Kindly, Is this correct?

Thanks

Mohamad