Thank you, Doug! One last question: - Using which command would one construct the "?h.white -1mm surface" and the "?h.white+30%GM surface" for visualisation purposes as in Salat Figure 1 ( http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ihub )?
Thank you! Markus 2014-03-26 15:36 GMT+01:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > > On 3/26/14 8:24 AM, Markus Gschwind wrote: > > Dear Doug and Bruce, > > I have three more questions concerning 'pctsurfcon'. > > 1) The inner sampling distance is set to 1mm by default, but the outer > sampling is done at a 30% of the cortical thickness. I saw that I could > easily change the parameters or modify the script, but I wonder why this > has been chosen like this. What was the rationale? > > A fixed distance of 1mm was used to help prevent the WM sample from > projecting so far back that it samples GM "behind" it. I can't remember how > I choose 30% (instead of 50%). I think David Salat used slightly different > parameters in his paper. > > > 2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in > order to get some group stats, right? > > Yes > > > 3) Is it also possibe to run the xhemi on the w-g.pct.mgh file? > > Yes > doug > > > > Thank you so much! > Markus > > > 2014-03-24 23:51 GMT+01:00 Markus Gschwind <markus.gschw...@gmail.com>: > >> 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. 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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 >>> >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. 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