$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 <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> 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
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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