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 <fis...@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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