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