Thank you Bruce, this works great. This is just for the records:
$ mris_expand -thickness surf/lh.white 0.35 surf/lh.white_outer0.35GM > using distance as a % of thickness > expanding surface surf/lh.white by 35.0% of thickness and writing it to > surf/lh.white_outer0.35GM > > $ mris_expand surf/lh.white -1 surf/lh.white_inner1mmWM > expanding surface surf/lh.white by -1.0 mm and writing it to > surf/lh.white_inner1mmWM Thanks again! 2014-03-27 13:29 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Markus > > use mris_expand. > > cheers > Bruce > > On Thu, 27 Mar 2014, Markus Gschwind wrote: > > 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=ihu >> b)? >> >> 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. 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 >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://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. 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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