Hi!
I have to do brain parcellation on rats and I am looking for a software/tool to do it. Right now I have only found tools for human brains. 

Thanks a lot!

Regards, 

Shandra

Would like to do the parcellation manually? In principle you could use the same tools. You can try ITKSNAP, AVIZO, AMIRA for this purpose.

If you want to do the parcellation (semi) automatically you could use one of the publicly available atlases and do registration based segmentation.

Good luck!

Alexandra

Hi Shandra,
I have used MIVA in the past which gives you manual anatomical registration based segmentation. You can give it a try.
http://rl-js.wpi.edu/miva.html
Regards,
Pallavi

Thanks a lot for the rapid responses. I was looking for an automatic method, but the semi-automatic should wok also. 

Regards,
Shandra

Hi Shandra,

I've never done what your looking for in rats, but I know freesurfer parcellates human brains. So, what if you change the MNI human atlas (which freesurfer uses) by a rat atlas, and then parcellate with freesurfer. This is the LONI rat atlas: 
http://www.loni.ucla.edu/Atlases/Atlas_D...

I hope it works for you.

Regards,

Hi Pallavi,

I want to try use MIVA, but the web don't link.
Have a new web address?

Regards,
David 

Hi,
I am new to this site. I downloaded the SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.11 and ITK-SNAP viewer. However, I cannot find the S1BF parcellation shown in this paper (Fig. 5) Barriere et al 2019 (https://doi.org/10.1038/s41467-019-13575...).

Any advice is appreciated,
John