open-discussion > Rat Brain Parcellation
Showing 1-7 of 7 posts
Display:
Results per page:
Nov 20, 2013  04:11 AM | Shandra Gutierrez
Rat Brain Parcellation
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
Nov 20, 2013  06:11 AM | Alexandra Badea
Rat Brain Parcellation
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
Nov 20, 2013  07:11 AM | Pallavi Rane
RE: Rat Brain Parcellation
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
Nov 22, 2013  01:11 AM | Shandra Gutierrez
RE: Rat Brain Parcellation
Thanks a lot for the rapid responses. I was looking for an automatic method, but the semi-automatic should wok also. 

Regards,
Shandra
Nov 22, 2013  04:11 AM | David Cardenas
RE: Rat Brain Parcellation
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,
Jan 7, 2014  10:01 AM | Shih-Hsien Yang
RE: Rat Brain Parcellation
Hi Pallavi,

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

Regards,
David 

Oct 9, 2020  07:10 AM | John Seymour - University of Texas Health Science Center
RE: Rat Brain Parcellation
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