Hi Cirong, Thanks so much for your kind and helpful introduction. The moneky used in my study is Macaca fascicularis and I would like to use a published temple you mentioned (http://purl.org/net/kbmd/cyno). However, the downloadable image is Analyze format, not NIFTI that I need though. For the new wfu_pickatlas, it does include a primate atlas for rhesus monkey, but not for fascicularis. I think it might be not good for my study.
Best, Liang 2010/11/17 Liu Ci-Rong <[email protected]> > What do you mean by the standard space? > There are is no the standard space in monkey image community right now. > > If you look through the former studies related to monkey image, they > usually created study-specific monkey template based on monkey subjects they > used. The coordinate of those templates were always registered to one of the > following atlas: > 1.A Combined MRI and Histology Atlas of the Rhesus Monkey Brain by > Kadharbatcha S. Saleem and Nikos K. Logothetis > 2.Pimate Brain Maps: Structure of the Macaque Brain (Elsevier, Amsterdam, > 2000) > 3.The Rhesus Monkey Brain in Stereotaxic Coordinates by Paxinos, Huang, and > Toga. > (*You can regard one of them as the standard space*) > > If you don't want to make study-specific monkey template of your own, there > are several well-defined template you can use: > 1. For Macaca mulatta: > http://brainmap.wisc.edu/monkey.html > 2. For Macaca fascicularis : > http://purl.org/net/kbmd/cyno > > If your monkey are rhesus macaques, the first template is strongly > recommended and it had been registered to Saleem's altas. Right now, I have > successfully used this templates to normalize and co-register my monkey fMRI > data with FSL. > ~~ > ~~ > For the AAl-like, or Region-labeled atlas, you can find one in the newest > version of http://www.nitrc.org/projects/wfu_pickatlas/ > A monkey Region-labeled atlas is available in that software, but "its > cortical boundaries are non-specific (e.g. prefrontal cortex is treated as > one continuous region instead of being split into dorsal, orbital, and > ventral components)". > > For more specific parcellation atlas, our group are gonna make one based on > coordinates of Saleem's atlas. Meanwhile, one group of Wisconsin University > is making a atlas based on Paxinos's coordinates as far as I know. > > > > > > On Wed, Nov 17, 2010 at 2:00 AM, > <[email protected]>wrote: > >> Send caret-users mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> >> Today's Topics: >> >> 1. Parcellation for macaque brain (liang wang) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 16 Nov 2010 01:37:03 -0500 >> From: liang wang <[email protected]> >> Subject: [caret-users] Parcellation for macaque brain >> To: "Caret, SureFit, and SuMS software users" >> <[email protected]> >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> I am curious whether there is region parcellation or standard atlas for >> macaque brain, such as AAL template in human brain. Also, does caret >> provide >> a macaque brain image in a standard space, in which we can conduct group >> analysis. If any, hopefully this image could be identified by AFNI/FSL. . >> >> Thanks, >> Liang >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://brainvis.wustl.edu/pipermail/caret-users/attachments/20101116/7af4aff0/attachment-0001.html >> >> ------------------------------ >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> End of caret-users Digest, Vol 86, Issue 8 >> ****************************************** >> > > > > -- > Best Regards, Liu Ci-Rong > ================= > Liu Ci-Rong, > Ph.D. Candidate, Kunming Institute of Zoology, CAS, Kunming, China > Visiting Scholar, Institute of Biophysics, CAS, Beijing, China > Visiting Scholar, National Laboratory of Pattern Recognition, CAS, Beijing, > China > Address: 15 Datun Road, Chaoyang District, Beijing 100101, China > Email: [email protected] > ===================== > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
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