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| ## 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>> |
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| mri_segment | |
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| mri_segment - segments the white matter (based on voxel value) out of the brain volume to produce the wm volume | = Description = This program segments white matter from the input volume based on voxel value to produce the wm 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 |
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| command argA argB -flag1 <arg1> -flag2 <arg2> -flag3 <arg3> | mri_segment <classifierfile> <invol> <outvol> [options] |
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| = Positional Arguments = argA |
= Arguments = == Positional Arguments == || <classifierfile> || classifier file || || <invol> || input volume || || <outvol> || output volume || |
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| Description argB Description = Required Flagged Arguments = -flag1 <arg1> Description - flag2 <arg2> Description = Optional Flagged Arguments = -flag3 <arg3> Description. |
== 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|| |
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| file1 | || <outvol> || output volume || |
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| Description | |
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| file2 | = Examples = |
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| Description | == Example 1 == {{{ mri_segment brainmask.mgz wm_test.mgz -wlo 80 }}} 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 |
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| = Example 1 = command argA argB -flag1 foo -flag2 goo Description = Example 2 = command argA argB -flag1 foo -flag2 goo -flag3 hoo Description |
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| ["command2"] ["command3"] = Author = JaneSmith |
[[recon-all]] [[mri_fill]] |
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| Command``Guide | FreeSurfer |
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| = References = ## For example: ["Belliveau1991"] NameYear |
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| Report bugs to <> | Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
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| = Category = ## For example: CategoryFreeSurferCommandVolumeConversion Category``Stream``Command |
= Author/s = BruceFischl |
Index
Contents
Name
mri_segment
Description
This program segments white matter from the input volume based on voxel value to produce the wm 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
Synopsis
mri_segment <classifierfile> <invol> <outvol> [options]
Arguments
Positional Arguments
<classifierfile> |
classifier file |
<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 |
Outputs
<outvol> |
output volume |
Examples
Example 1
mri_segment brainmask.mgz wm_test.mgz -wlo 80
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
See Also
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>