I think that the first option you provided is more along the lines of what I'm looking for. Thanks
Corinna On Mon, Nov 4, 2013 at 5:37 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Yes. As Bruce mentioned you can also use the program that creates the > wmparc (mri_aparc2aseg). You can look in the recon-all.log file for the > command line (there will be two in there, one to create aparc+aseg and one > to create wmparc). You can run this command with --wmparc-dmax to set the > maximum distance from cortex to dilate the voxels. Make sure to name the > output something other than wmparc.mgz so you don't overwrite what is > there. When it is done, there will be a WM label for each cortical label. > Is this what you want? It won't do this for subcortical structures. > doug > > > On 11/04/2013 12:25 PM, Corinna Bauer wrote: > >> ok thanks, I'll give that a try. I would have to do that for each of the >> segmentations of interest and I get the number from the LUT? >> >> >> On Mon, Nov 4, 2013 at 11:47 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> There is not a single command to do it, but you could do something >> like >> >> mri_binarize --i aparc+aseg.mgz --wm --o wmmask.mgz # mask of >> white matter >> mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 >> mri_binarize --i seg.mgz --match 17 --dilate 2 --o mask17.dil2.mgz # >> mask of seg 17 dilated by 2 voxels >> fscalc wmmask.mgz and mask17.dil2.mgz --o mask17.dil2.wm.mgz # seg 17 >> inside WM >> mri_concat mask17.mgz mask17.dil2.wm.mgz --sum --o mask17+wm.mgz >> # seg >> 17 plus dilation into WM >> >> doug >> >> >> On 11/04/2013 11:38 AM, Corinna Bauer wrote: >> > Hello all, >> > Is there a way to expand a GM label into the white matter by n >> voxels? >> > >> > Corinna >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 <mailto: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. >> >> >> > -- > 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/ > >
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