Hi Colin,
We are transitioning to using FreeSurfer only for segmentation (though Caret5 will not be going away). I have chimpanzee and macaque interests as well however, so I will make FreeSurfer run with these (I have big enough datasets that I plan to actually replace FreeSurfer's templates with ones based on my subjects for non-human primates). If you would like to be involved in that process, let me know and we can talk about it further off list. Peace, Matt. _____ From: [email protected] [mailto:[email protected]] On Behalf Of Colin Reveley Sent: Friday, March 30, 2012 2:57 PM To: [email protected] Subject: [caret-users] segmentation Hi - I know there is a new version of caret in the works, and I know that it is part of the connectome project, and therefore will likely have more features related to tractography. I'm looking forward to that hugely. I was wondering what features it might have regarding segmentation. Caret is the easiest, fastest and most reliable way to segment an MRI to a good surface (certainly for macaque) that I've worked with. But the segmentation is midthickness. Will the new version segment at the GM/WM boundary and make midthickness and pial surfaces from there? When doing surface based tractography with FSL, using a WM surface that's registered to F99 is really great. But hard to make (one must do it in freesurfer, which is not designed for monkey). And, I was wondering: with good quality diffusion data, the GM/WM boundary region is often visible as an identifiable band in FA, westin and other tensor maps. In an ideal world, one would position the surface exactly on that band so that the uncertainty at the boundary can be avoided when seeding/targeting cortical regions from surface data. Perhaps there would be a way to do that? It would be of tremendous interest to me to know what plans there are in regard to this, and if, in general, the new caret will drop anything in terms of features that is relevant to segmentations, surface registration and all things macaque. And, if things are dropped whether caret5 will be maintained. best, Colin
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