Index

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

Author/s

BruceFischl

mri_segment (last edited 2021-04-20 16:13:19 by AndrewHoopes)