--o outstem

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

--reg regfile

Can be LTA or reg.dat

--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)

--no-aseg

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

--no-fill-csf

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)

--mgz

Use mgz format (default)

--mgh

Use mgh format

--nii

Use nii format

--nii.gz

use nii.gz format

--ttype+head

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'

--debug

Turn on debugging

--checkpots

Don't run anything, just check options and exit

--help

Print out information on how to use this program

--version

Print out version and exit