Re: [Freesurfer] expand GM label into white matter

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

Re: [Freesurfer] expand GM label into white matter

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 wrote: > I think that the first option you provided is more along the lines of what > I'm looking for. Thanks > > Corinna > > >

Re: [Freesurfer] expand GM label into white matter

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 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

Re: [Freesurfer] expand GM label into white matter

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 maxi

Re: [Freesurfer] expand GM label into white matter

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 wrote: > > There is not a single command to do it, but you could do something like > > mri_binarize --i aparc+ase

Re: [Freesurfer] expand GM label into white matter

Hi Corinna I think this what Doug's WM parcellation tool does cheers Bruce On Mon, 4 Nov 2013, 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 Fre

Re: [Freesurfer] expand GM label into white matter

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

[Freesurfer] expand GM label into white matter

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended