Index
Contents
Name
mri_fill
Synopsis
mri_fill [options] <input MR directory> <output MR directory>
Arguments
Positional Arguments
<input MR directory> |
input directory |
<output MR directory> |
output directory |
Required Flagged Arguments
none
Optional Flagged Arguments
General
-T <threshold> |
specify fill_holes threshold (default=1) |
-xform <xformname> |
use xform dst offset to get an accurate Talairach volume |
-segmentation <filename> |
aseg volume used to perform fill |
-atlas <filename> |
specify atlas to use for auto-filling |
-fillven |
fill ventricles |
Seed point options in Talairach coordinates
-C <x> <y> <z> |
Talairach coords of the seed for the corpus callosum |
-P <x> <y> <z> |
Talairach coords of the seed for the pons |
-lh <x> <y> <z> |
Talairach coords of the white matter seed for the left hemisphere |
-rh <x> <y> <z> |
Talairach coords of the white matter seed for the right hemisphere |
Alternative seed point options in voxel coordinates
-CV <x> <y> <z> |
voxel coords of the seed for the corpus callosum |
-PV <x> <y> <z> |
voxel coords of the seed for the pons |
Outputs
filled |
The filled volume for the cortical reconstruction- used for subsequent surface tesselation. |
Description
This program creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation.
Examples
Example 1
mri_fill SUBJECT/mri/wm/. SUBJECT/mri/filled
Takes a subjects wm volume as input and uses this to find cutting planes to seperate the hemispheres and remove the brainstem, and fills hemispheres with specific values as filled volume output.
Bugs
See Also
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>