Hi Monica, See inline replies below.
Donna On 09/21/2010 07:21 PM, Wey, Hsiao-Ying Monica wrote: > Dear all, > > I am a beginner for Caret Software and am quite exciting about this > amazing tool. > I have some questions and would like to seek for advises. > > My attempt of using Caret is to overlay fMRI activation maps (Map > Volumes to Surfaces) and make comparison across species. > I processed my fMRI data using FEAT analysis in FSL. > However, my situation is a little bit complicated. > Because instead of comparing macaque with human, I'm comparing baboon > with human. > In this case, we don't have an atlas for baboons, but I do have a > group-averaged baboon brain template generated in-house. > > Two major questions that I have are > > (1) How can I map the activations (z-stats) onto to the baboon brain > template that I have, since there is no baboon atlas in Caret that I > can use? I just learn from the e-mail lists that I could generate the > surface map (of the template) using Freesurfer, and use Caret to > overlay activations onto it. Is it the correct way of doing it? I've heard of people segmenting average MRI, but unless your average structural volume is as crisp and clear as the atlas target used with something like FSL's FNIRT, I wouldn't get my hopes up for a good result. Actually, what we do instead is segment the individuals; register the surfaces to a common target; and then average in surface-land. In this case, it isn't clear what that common target would be, but this route still seems preferrable. > If I want to make comparisons between human and baboon (with the same > stimulation), any suggestions on how to do this properly? I feel like > to generate a baboon brain atlas might be the best way, although it > seems to be very difficult. As far as I know, David Van Essen is the only person brave enough to do this. > Are there instructions on how to make the atlas myself using the > template I have? Or, following the methods as described in the > "Contours and Selections" manual is the most appropriate way? No, probably not. David's working on a paper that might help. Meanwhile, his PALS paper 2005 (see our publications link) describes how he did it for humans. > > (2) The area expansion map between macaque and human inside the > tutorial looks interesting. Any suggestions/hints/instructions on how > to generate those? David's forthcoming paper will probably detail this. You might also have a look at our PNAS paper (Jason Hill, et. al. 2010). > > Any comments are appreciated. Thank you all for you time! > > > Best, > Hsiao-Ying (Monica) > > ------ > Hsiao-Ying (Monica) Wey, B.Sc. > PhD Candidate > Research Imaging Institute > Department of Radiology > UT Health Science Center at San Antonio > Email: [email protected] <mailto:[email protected]> > Phone: (210) 567-8163 [7-8163] > > "Hard work keeps the wrinkles out of the mind and spirit." > ~Helena Rubinstein > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
