Hi Doug, Is 'pctsurfcon' intended to supersede 'mri_cnr'? If not, what are the intended situations in which one would be used over the other?
thanks, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 3/24/14 5:21 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
you might want to look at the pctsurfcon script to see if that gets you where you want to be
On 03/24/2014 06:18 PM, Bruce Fischl wrote:
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 fischl@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 <fischl@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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