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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. 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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| command argA argB -flag1 <arg1> -flag2 <arg2> -flag3 <arg3> | mri_segment [options] <invol> <outvol> |
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| = Positional Arguments = argA |
= Arguments = == Positional Arguments == || <invol> || input volume || || <outvol> || output volume || |
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| 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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| argB | = Example = |
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| Description | {{{ 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 |
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| = Required Flagged Arguments = -flag1 <arg1> Description - flag2 <arg2> Description = Optional Flagged Arguments = -flag3 <arg3> Description. = Outputs = file1 Description file2 Description = Example 1 = command argA argB -flag1 foo -flag2 goo Description = Example 2 = command argA argB -flag1 foo -flag2 goo -flag3 hoo Description = See Also = ["command2"] ["command3"] = Author = JaneSmith = Links = Command``Guide = References = ## For example: ["Belliveau1991"] NameYear = Reporting Bugs = Report bugs to <> = Category = ## For example: CategoryFreeSurferCommandVolumeConversion CategoryFreeSurferCommandSegmentation |
= Author/s = BruceFischl |
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