mri_segment
mri_segment <classifierfile> <invol> <outvol>
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 invol outvol -conform
| Argument | Explanation |
|---|---|
| <classifierfile> | classifier file |
| <invol> | input volume |
| <outvol> | output volume |
| Argument | Explanation |
|---|---|
| -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 1 and 255. voxels of value 1 will be 'deleted' and voxels of value 255 will be 'filled' |
| -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 |
| Output | Explanation |
|---|---|
| <outvol> | output volume |
Report bugs to <freesurfer@nmr.mgh.harvard.edu>