oh, those should be embedded in the .annot file it creates
On Wed, 9 Apr
2014, Corinna Bauer wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, 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
<gr...@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
> <gr...@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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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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