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

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

Links

FreeSurfer

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

BruceFischl

-  ⇤ ← Revision 5 as of 2004-08-10 13:37:09 → 
  Size: 1253
  Editor: DavidTuch
  Comment: updated formatting
+   ← Revision 14 as of 2017-12-04 12:46:06 → ⇥
  Size: 2901
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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
##
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-##
## Note: If you are modifying this page please refer to the
## CommandTemplate page and confirm that this page has the latest
## CommandTemplate formatting
+'''Index'''
<<TableOfContents>>
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-mri_segment - segments the white matter (based on voxel value) to produce the wm volume
+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
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-mri_segment [argA] -flag1 [arg2] -flag2 [arg3] [<options>]
+mri_segment <classifierfile> <invol> <outvol> [options]
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-= Positional Arguments =
|| [argA] || description ||
+= Arguments =
== Positional Arguments ==
|| <classifierfile> || classifier file ||
|| <invol> || input volume ||
|| <outvol> || output volume ||
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+Line 27:
-= Required Flagged Arguments =
|| -flag1 [arg1] || description ||
|| -flag2 [arg2] || 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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-= Optional Flagged Arguments =
|| -flag3 [arg3] || description ||
|| -flag4 [arg4] || description ||
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-|| volume1 || description ||
|| volume2 || description ||
+|| <outvol> || output volume ||
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-= Description =
description
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+Line 57:
-= Example 1 =
command foo -i f -o out
+= 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 2 =
command foo -i f -o out -f fvalue

description
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-["othercommand1"], ["othercommand2"]

= Author/s =
JaneSmith
+[[recon-all]]
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-FreeSurfer, FsFast
+FreeSurfer
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-= References =
["References/Lastname###"]
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-= Methods Description =
{{{
description
description
}}}

= Category =
CategoryFreeSurferCommandsSegmenation
+= Author/s =
BruceFischl