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Dear Rashmi, If you need any help with the MRI template of Schwarz et al 2006 just let me know. I got quite familiar with it when working in our SAMIT toolbox, and I have all the original files, plus some modifications that we did for our lab. @Helmut: Thanks for the list of templates, I was not aware of some of them. More images to play with in the next days. Best regards, David Vállez On Wed, Jun 17, 2015 at 5:50 PM, H. Nebl <[log in to unmask]> wrote: > Dear Rashmi, > > For the Karolinska rat template see > http://expmr.ki.se/research/ratatlas.jsp However, I would not rely on > this template, it's an old and low-resolution one. For recent multi-subject > high-res rat templates see > > - spmratIHEP toolbox including an template based on 21 SP rats (Nie et > al., 2013, Hum Brain Mapp, https://dx.doi.org/10.1002/hbm.21511 , 2014, > PLOS ONE, https://dx.doi.org/10.1371/journal.pone.0108295 , you'll have > to contact the senior author to receive a copy of the toolbox) > - the CERMEP (Lyon, France) template based on 7 (12?) SD rats (Lancelot et > al., 2014, PLOS ONE, https://dx.doi.org/10.1371/journal.pone.0109113 ) > - SAMIT by Vállez Garcia et al. (2015, PLOS ONE, > https://dx.doi.org/10.1371/journal.pone.0122363 ), for download see > http://mic-umcg.github.io/samit/ , there are some PET and SPECT > templates based on a mixture of Wistar and SD rats, but it also includes an > SD T2 template from Schwarz et al. (2006, > https://dx.doi.org/10.1016/j.neuroimage.2006.04.214 ), > - Wistar Rat MRI Atlas from Kawashima lab (Valdés-Hernández et al., 2011, > Front Neuroinform, http://dx.doi.org/10.3389/fninf.2011.00026 ) which can > be obtained from http://www.idac.tohoku.ac.jp/bir/en/db/rb/101028.html > - the template described in Gaser et al. (2012, Neuroimage, > https://dx.doi.org/10.1016/j.neuroimage.2012.06.066 , try to contact > Christain Gaser), again Wistar > > It's not obvious which of these templates is optimal for your purpose, > you'll have to give a try on all of them probably. Possibly you might > prefer to go with a Wistar template even if you scan SD rats to better > match contrast/resolution/type of scanner. There are several other high-res > atlases like the Waxholm Space atlas > http://software.incf.org/software/waxholm-space-atlas-of-the-sprague-dawley-rat-brain > which provide reference files in nii (or nii-compatible) format, these > might also be useful, although in general, a multi-subject atlas should be > preferable (if you need anatomical labels for particular brain regions > available in only one of the atlases it should be possible to coregister > them onto other atlases / templates). > > Best > > Helmut >