That command will work. There's no need to include the mask. Also, I would add --seg-erode 2 which will erode each segmentation by 2 voxel (1mm3) to make sure you avoid partial voluming. That feature might not be available in 5.3, but I can get you a version that does if not doug

On 07/20/2014 01:50 AM, Alshikho, Mohamad J. wrote:

Hi Dear Fs Experts I will post my question again, hopefully I can find an answer :)

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

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