This command computes the partial volume fractions for cortex, subcortical GM, WM, and CSF. This command will create a voxel map with the percent of each tissue class in each voxel.


mri_compute_volume_fractions [options] --o <outstem> --reg <regfile>


Required Flagged Arguments

--o outstem

Output will be outstem. {cortex, subcort_gm,wm,csf}.mgz

--reg regfile

Can be LTA or reg.dat

Optional Flagged Arguments

--usf USF

Upsample factor (default is 2)

--regheader subject

--r res

Resolution, sets USF = round(1/res)

--seg segfile

Use segfile instead of aseg.mgz

--wsurf wsurf

White surface (default is white)

--psurf psurf

Pial surface (defualt is pial)


Do not include aseg (good for testing)

--stack stackfile

Put ctx, subcortgm, wm, csf into a single multi-frame file

--gm gmfile

Put ctx+subcortgm into a single-frame file


Do not attempt to fill voxels surrounding seg with the extracerebral CSF segmentation. NOTE: when the fill is done, there is no attempt to actually segment xCSF voxels. The passed segmentation is dilated and the new voxels become xCSF. If the passed seg already has the CSF_ExtraCerebral seg, nothing will be done.

--dil N

For xCSF fill, dilate by N (default is 3), use -1 to fill the entire volume

--out-seg outseg

Save seg (after adding xcsf voxels)

--ttseg ttseg

Save tissue type segmentation (probably not that useful)

--ttseg-ctab ctab

Save tissue type segmentation ctab (probably not that useful)


Use mgz format (default)


Use mgh format


Use nii format


use nii.gz format


Use default+head instead of default tissue type info for seg

--vg-thresh thrshold

Threshold for 'ERROR: LTAconcat(): LTAs 0 and 1 do not match'


Turn on debugging


Don't run anything, just check options and exit


Print out information on how to use this program


Print out version and exit


See Also



FreeSurfer, FsFast

Reporting Bugs

Report bugs to <>

mri_compute_volume_fractions (last edited 2017-12-11 11:58:37 by MorganFogarty)