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'''Index'''
<<TableOfContents>>


= Name =
mri_compute_volume_fractions

= Description =
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. 

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

= Arguments =
== 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) ||
||--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 ||


= Bugs =

= See Also =
[[mri_compute_volume_intensities]]

= Links =
FreeSurfer, FsFast

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>