it really depends on the size of the abnormality. I would guess 2 is too
big, and you want something more like 1, and sampling not averaging
On Mon,
24 Mar 2014, Markus Gschwind wrote:
Hi Bruce!
Ok I see, great! Tank you!
So to double check, this will be something like :
mri_vol2surf \
--mov /mri/nu.mgz \
--ref /mri/nu.mgz \
--surf /surf/lh.white
--projdist mmdist -2 \ # for inside white
# --projdist mmdist 2 \ # for outside white
--interp trilinear \
--hemi lh \
--out lh.nu_inside_white.mgh
I am not sure which one to use from those, as I want to compare stable
values but distant from white.
--projfrac-avg min max del : average along normal
--projdist mmdist : distance projection along normal
--projdist-avg min max del : average along normal
What would you recommend?
Thank you again!
Markus
2014-03-24 21:29 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi Markus
I wouldn't use brainmask as it has been normalized too
aggressivley. Maybe the nu.mgz. Look at the difference between
values just outside of it and just inside of it
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind wrote:
Dear Bruce,
Thanks for the rapid answer!
Do you mean that I take the voxel values of
brainmask.mgz at the place where
the ?h.white surface passes, right?
I thought that the ?l.white surface marks the limit
between GM and WM as a
result of a binary decision.
I would be interested in the local certainty of this
decision. I thought
this is represented by the slope between the values
around 70 and those
>100.
Thanks again,
Markus
2014-03-24 19:26 GMT+01:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Markus
I would think that looking at the gray/white
contrast across the
?h.white surface would be more informative
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind wrote:
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
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