Dear all,
I would like to capture regions where the gray matter/ white matter junction is blurred in order to detect possible focal cortical dysplasias.
As I understood the WM/GM segmentation is done by the script mri_segment.
Would it be possible detect those regions where the gradient between GM and WM regions is low?
I imagined that running mri_segment several times, with each time a different lower GM threshold and higher WM threshold, and then calculating the diference between the results, might give such information.
I am very much interested in what you think about this approach and how to do it practically.
For info here are the optional flags of mri_segment:
-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
Thank you very much for all comments!
Markus