## Note: This page was created with the CommandTemplate
##
## If you're modifying this page please take a look at the
## latest version of CommandTemplate to ensure that you're
## using the latest version of the CommandTemplate
##
## See HelpOnCommandTemplate for description of formatting

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


= Name =
mris_volmask - computes a volumetric mask based on the white and pial surfaces. The mask contains 4 labels, namely LEFT_WHITE, LEFT_GREY, RIGHT_WHITE, RIGHT_GREY, which are computed based on the white and pial surfaces. 

= Synopsis =
mris_volmask [ options ] subject

= Arguments =
== Positional Arguments ==
|| subject || subject name || recon-ed directory in the SUBJECTS_DIRECTORY ||

== Options (Optional Flagged Arguments) ==
|| --surf_white argWhite || root name for the white surfaces (default white) || by default, the white surfaces considered will be <subject>/surf/<hemi>.<argWhite>  ||
|| --surf_pial argPial || root name for the pial surfaces (default pial) || by default, the pial surfaces considered will be <subject>/surf/<hemi>.<argPial> ||
|| --out_root argRoot || root name for the output file (default ribbon) || by default, <subject>/mri/<argRoot>.mgz ||
|| --save_ribbon || option to add saving ribbon masks for each of the hemispheres || if present, two new files will be written upon exit, namely <subject>/mri/<hemi>.<argRoot>.mgz, with hemi taking the values lh and rh, respectively; only the cortical ribbons will be saved if this option is used ||
|| --save_distance || option to save the distance from one surface || if present, this option will cause 4 new files to be written in <subject>/mri, namely <subject>/mri/<hemi>.dwhite.mgz and <subject>/mri/<hemi>.dpial.mgz (NB: the distance will be signed and will only be accurate within a range specified by the cap_distance argument ||
|| --label_background argBkg || value for the background in the ribbon.mgz output || default is 0 - this only affects the main output ||
|| --label_left_white argLhWhite || value for the left white matter label in the ribbon.mgz output || default is 20 - only affects the main output ||
|| --label_left_ribbon argLhRibbon || value for the left grey matter label in the ribbon.mgz output || default is 10 - this only affects the main output ||
|| --label_right_white argRhWhite || value for the right white matter label in the ribbon.mgz output || default is 120 - only affects the main output ||
|| --label_right_ribbon argRhRibbon || value for the right grey matter label in the ribbon.mgz output || default is 110 - this only affects the main output ||
|| --cap_distance value || maximum distance at which the signed distance function from a surface is computed || default value is 3 ||
 
= Outputs =
|| ribbon.mgz || mask (having the same resolution as brain.mgz) containing 4 labels, for the white and grey matter of each hemisphere ||
|| lh.ribbon.mgz || optional output (triggered by the --save_ribbon option) which only marks the ribbon for the left hemisphere ||
|| rh.ribbon.mgz || optional output (triggered by the --save_ribbon option) which only marks the ribbon for the right hemisphere ||
|| lh.dwhite.mgz || optional output (triggered by the --save_distance option) which saves the distance from the left white surface ||
|| lh.dpial.mgz || optional output (triggered by the --save_distance option) which saves the distance from the left pial surface ||
|| rh.dwhite.mgz || optional output (triggered by the --save_distance option) which saves the distance from the right white surface ||
|| rh.dpial.mgz || optional output (triggered by the --save_distance option) which saves the distance from the right pial surface ||


= Description =
This binary uses the white and pial surfaces to determine if a voxel (of brain.mgz) is part of the ribbon or white matter.
All the outputs of this program will have exactly the same resolution and RAS parameters as the original <subject>/mri/brain.mgz file.

The algorithm computes the signed distance function from each of the white and pial surfaces and then uses the sign to determine which set a voxel belongs to.

= Examples =
== Example 1 ==
mris_volmask bert

Computes the ribbon.mgz for subject bert

description

== Example 2 ==
mris_volmask --save_ribbon bert

Computes the files ribbon.mgz and lh.ribbon.mgz, respectively rh.ribbon.mgz for subject bert.

= Bugs =
None

= See Also =
[[mri_aparc2aseg]]

= Links =
FreeSurfer, FsFast


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

= Author/s =
Gheorghe Postelnicu