On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz

doug

On 04/10/2014 09:52 AM, Corinna Bauer wrote:
> For creating corresponding wm segmentations to the rois derived from
> mris_divide_parcellation, should mri_aparc2wmseg be used or should I
> follow the steps outlined in this posting
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
> ?
>
> Thanks
>
> Corinna
>
>
> On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinnab83@gmail.com

> <mailto:corinnab83@gmail.com>> wrote:
>
> Perfect. Thanks!
>
>
> On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> you'll need to figure it out from the volume itself by loading
> the seg
> with both -seg and -aux. When you find the label you want,
> click on it
> and the aux value in the control window will tell you what the
> id is
>
> doug
>
> On 04/09/2014 09:41 AM, Corinna Bauer wrote:
> > In the mri_extract_label, there is a label number. Where
> would I find
> > this for the new labels?
> >
> > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
> >
> >
> > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > yep, exactly
> >
> >
> > On 4/8/14 6:00 PM, Corinna Bauer wrote:
> >> Hi Doug,
> >> After I have the labels then in each subject's T1
> space, I will
> >> need to then put them into diffusion and resting state
> space.
> >>
> >> I already have scripts that put the parcellations into
> >> subject-specific diffusion/resting state space (using
> bbregister,
> >> tkregister2, mri_vol2vol (using the inverse
> registration from
> >> bbregister to put the T1 into diffusion space),
> mri_extract_label
> >> (extract labels from aparc+aseg.mgz), and then
> mri_label2vol
> >> (register each of the extracted labels into diffusion
> space).
> >> Would a similar approach work for the new labels?
> >>
> >> Corinna
> >>
> >>
> >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
> >> <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >>
> >>
> >> Exactly what you have described won't work very
> well because
> >> it would be
> >> in the volume. I would divide up the parcellations in
> >> fsaverage space
> >> like you've done, then map the parcellation to each
> subject using
> >> mri_surf2surf (--sval-annot, see example 6)
> >>
> >> doug
> >>
> >> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> >> > Hello all,
> >> >
> >> > I am planning to use mris_divide_parcellation to
> split the
> >> Desikan
> >> > atlas into smaller ROIs, but will need the new
> ROIs to be
> >> consistent
> >> > between subjects.
> >> >
> >> > Can I achieve this if I register each subject to
> fsaverage
> >> space and
> >> > then apply the inverse transform to the divided
> >> parcellations (which
> >> > are currently done on the fsaverage brain)?
> >> >
> >> > If so, for extracting each label, what would be
> used for
> >> the label
> >> > number?
> >> > (i.e. mri_extract_label
> ${subj_dir}/mri/aparc+aseg.mgz *2035*
> >> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
> >> >
> >> >
> >> > Thanks
> >> >
> >> > Corinna
> >> >
> >> >
> >> > _______________________________________________
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> >> >
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> >>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>
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> <tel:617-724-2358 <tel:617-724-2358>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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