Index

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

recon-all mri_fill

Links

FreeSurfer

Reporting Bugs

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

Author/s

BruceFischl