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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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