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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