External Email - Use Caution
Ok thanks for the suggestions.
On Sun, Oct 20, 2019 at 3:11 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionHi 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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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