Whow that is great!! Thank you so much Doug, I was not aware of this! That's what I needed it seems. Thanks Bruce and Doug! Markus
2014-03-24 23:21 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > 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 <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. > >> > >> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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