Index
Contents
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
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Author/s
Gheorghe Postelnicu