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
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