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: mha...@wustl.edu On 3/24/14 5:21 PM, "Douglas N Greve" <gr...@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 <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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
