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The 112RM-SL atlas can be used as a template in a standard space. One might not consider it a complete atlas as it does not yet contain any ROIs. Current work is ongoing to create ROIs to go along with the atlas. If one uses the 112RM-SL atlas, the coordinates can be used with the Saleem-Logothetis book to look up the regions. If anyone has their ROIs as an image overlaid on the 112RM-SL atlas, I have a program that would label the statistical peaks. In McLaren et. al. there is a linear transform from F99 to Saleem-Logothetis space. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Thu, Dec 9, 2010 at 12:08 PM, wolf zinke <[log in to unmask]>wrote: > CARET has the F99, D99, F6, atlases and a few others. >> > > > Hi, maybe one needs to clarify, whether atlas means atlas or template, or > kind of standard space. In my understanding, a standard space is not an > atlas. However, Caret offers several atlases for the macaque as well, e.g. > based on the Paxinos atlas. To use these atlasses in order to identify > regions, it works best for me to transform individual brains into the F99 > space with fnirt. Another Method I am using, is to transform individual > brains to the Saleem-Logothetis template, so I can directly use their > coordinates to identify regions. > However the other way around, creating rois of specific regions, I have no > dataset I rely on. Here I use my own anatomical rois that I created for one > monkey. I transform these to other monkeys and correct them manually. An > awful time consuming work to do... If someone has a better method at hand, I > would be very happy to hear about it. > > I think, it would be a great idea, if FSL could include both, a standard > template of a macaque brain, as well as a atlas. I hope that some of these > guys mentioned in the posts I linked to will provide an atlas soon, and that > this could be included in the FSL package. > > wolf >