just use aseg or aparc+aseg. btw 17 = left hippocampus On 11/18/2013 12:41 PM, Corinna Bauer wrote: > Hi Doug, I don't see anywhere a seg.mgz. > > mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 > > Corinna > > > On Tue, Nov 5, 2013 at 11:38 AM, Corinna Bauer <corinna...@gmail.com > <mailto:corinna...@gmail.com>> wrote: > > 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 <mailto: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> > <mailto: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> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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 <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/ > > >
-- 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
