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'''Index'''
<<TableOfContents>>

= 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