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| mri_segment - segments the white matter (based on voxel value) to produce the wm volume | mri_segment |
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| This program segments white matter from the input volume. The input volume should be normalized such that white matter voxels are ~110 valued, and the volume is conformed to 256^3. This can be accomplished by: mri_normalize <invol> <outvol> -conform | This program segments white matter from the input volume. The input volume should be normalized such that white matter voxels are ~110-valued, and the volume is conformed to 256^3. This can be accomplished by `mri_normalize -conform invol outvol`. Note that flagged options must be provided before positional arguments. |
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| mri_segment <classifierfile> <invol> <outvol> | mri_segment [options] <invol> <outvol> |
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| || <classifierfile> || classifier file || | |
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| || -nold_remove <s> ||don't run code that removes 1D strands from segmentation|| | |
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| = Outputs = || <outvol> || output volume || |
= Example = |
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= Examples = == Example 1 == ?? == Example 2 == ?? = Bugs = ?? = See Also = [[recon-all]] = Links = FreeSurfer = Methods Description = |
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| ?? | mri_segment -wlo 80 brainmask.mgz wm_test.mgz |
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= References = [[References/Lastname###]] ?? = Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
This example would segment the white matter voxels from brainmask.mgz with an intensity greater than 80. The new volume would be called wm_test.mgz |
Index
Contents
Name
mri_segment
Description
This program segments white matter from the input volume. The input volume should be normalized such that white matter voxels are ~110-valued, and the volume is conformed to 256^3. This can be accomplished by mri_normalize -conform invol outvol. Note that flagged options must be provided before positional arguments.
Synopsis
mri_segment [options] <invol> <outvol>
Arguments
Positional Arguments
<invol> |
input volume |
<outvol> |
output volume |
Optional Flagged Arguments
-nold_remove <s> |
don't run code that removes 1D strands from segmentation |
-slope <s> |
set the curvature slope (both n and p) |
-pslope <p> |
set the curvature pslope (default=1.0) |
-nslope <n> |
set the curvature nslope (default=1.0) |
-debug_voxel <x y z> |
set voxel for debugging |
-auto |
automatically detect class statistics (default) |
-noauto |
don't automatically detect class statistics |
-log |
log to ./segment.dat |
-keep |
keep wm edits. maintains all values of 0 and 255 |
-ghi, -gray_hi <h> |
set the gray matter high limit (default=100.000) |
-wlo, -wm_low <l> |
set the white matter low limit (default=90.000) |
-whi, -wm_hi <h> |
set the white matter high limit (default=125.000) |
-nseg <n> |
thicken the n largest thin strands (default=20) |
-thicken |
toggle thickening step (default=ON) |
-fillbg |
toggle filling of the basal ganglia (default=OFF) |
-fillv |
toggle filling of the ventricles (default=OFF) |
-b <s> |
set blur sigma (default=0.25) |
-n <i> |
set # iterations of border classification (default=1) |
-t <t> |
set limit to thin strands in mm (default=4) |
-v |
verbose |
-p <p> |
set % threshold (default=0.80) |
-x <filename> |
extract options from filename |
-w <w> |
set wsize (default=11) |
-u |
usage |
Example
mri_segment -wlo 80 brainmask.mgz wm_test.mgz
This example would segment the white matter voxels from brainmask.mgz with an intensity greater than 80. The new volume would be called wm_test.mgz