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Index

Name

mri_segment - segments the white matter (based on voxel value) to produce the wm volume

Synopsis

mri_segment <classifierfile> <invol> <outvol>

Arguments

Positional Arguments

<classifierfile>

classifier file

<invol>

input volume

<outvol>

output volume

Optional Flagged Arguments

-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

Description

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Examples

Example 1

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Example 2

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Bugs

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See Also

recon-all

Links

FreeSurfer

Methods Description

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References

References/Lastname### ??

Reporting Bugs

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

Author/s

BruceFischl

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