Index

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