Thanks a lot, Anjie, Helmut and Donald!I will follow your suggestions and give feedback once I worked out the procedure.Best,
Chao-GanOn Fri, Oct 4, 2013 at 10:07 AM, MCLAREN, Donald <[log in to unmask]> wrote:
One more comment,It seems that DARTEL would be unnecessary given smoothness of the rat brain. You can probably just use the segment or new segment routines to good your images normalized. Both use non-linear warps as well. It may also be the case that you don't need non-linear warpping to match the brains in rats.Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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406-2464 or email.On Fri, Oct 4, 2013 at 10:04 AM, H. Nebl <[log in to unmask]> wrote:Dear Chao-Gan,
Kawashima lab (Valdes-Hernandez et al.) has some templates as well as tissue probability maps. For details see http://www.idac.tohoku.ac.jp/bir/en/db/rb/ , basically you have to fill in two forms and then they send the files to you (maybe it's automatic by now, dunno).
Nie et al. (2013, Human Brain Mapping) provide another template, please contact the senior author Baoci Shan for further information (his mail address is given in the paper). I received a copy of their templates this way. Here's a PDF about their toolbox http://mrrcwiki.einstein.yu.edu/images/5/51/SPMRATIHEP.pdf As far as I remember they have been/are working on tissue probability maps as well.
Alternatively, you might want to try rSPM, which allows deformation-based normalisation and might be useful if your data doesn't have enough contrast to ensure a good segmentation http://dbm.neuro.uni-jena.de/rSPM/ The approach is described in Gaser et al. (2012, Neuroimage).
Best,
Helmut
--Chao-Gan YAN, Ph.D.Research ScientistThe Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962Center for the Developing Brain, Child Mind Institute, 445 Park Avenue, New York, NY 10022The Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience, New York University Child Study Center, New York, NY 10016-Initiating + Service NodeThe R-fMRI Network (RFMRI.ORG)