I see. Yes, a bunch of those are on our to-do list for segmentation but
we don't have anything distributable at the moment. You are probably
better off running some other nonlinear warping like ANTS or VoxelMorph
to propagate the labels.

cheers
Bruce
On Sat, 19 Oct 2019, Vinny K wrote:

>
>         External Email - Use Caution        
>
> Hi Bruce,
> I'm looking at diencephalic and midbrain structures and their various
> subdivisions for application to tractography.  I used the thalamic nuclei
> segmentation feature in the development version of FreeSurfer to obtain
> labeling of individual thalamic nuclei that is run in addition to aseg, which
> has worked out great.  However, for other deep brain structures such as the
> subthalamic or pontine nuclei (e.g. pedunculopontine), to my knowledge, aseg
> does not parcellate these out; however, they are available MNI space. 
> FreeSurfer gives an excellent registration of labeled atlas structures in
> patients with big ventricles, which I've had difficulty with using other
> registration tools.  I was wondering if there was a way that I could bring
> some of these labeled nuclei in MNI space into the patient's T1 space using
> FreeSurfer.
>
> Thanks,
>
> Vinny  
>
> On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
>       Hi Vinny
>
>       why do you need to brain structures from MNI space? Isn't the
>       aseg
>       sufficient? Or are there structures that are not in the aseg?
>
>       cheers
>       Bruce
>       On Sat, 19 Oct
>       2019, Vinny K wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > Hi,
>       > FreeSurfer does a great job in registering atlas structures to
>       patients with
>       > big ventricles.  I'd like to use the calculated FreeSurfer
>       transforms in
>       > bringing additional subcortical structures from MNI space
>       (either MNI305 or
>       > MNI2009b) into native T1 space.  Can you please advise on how
>       to do this?
>       >
>       > Thanks,
>       >
>       > Vinny  
>       >
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