Rat fMRI data registration to standard template

Dear AFNI experts,

I am new to rat data analysis and I wanted to register rat fMRI data to standard template, I understand that the method in “Registering and Analyzing Rat fMRI Data in the Stereotaxic Framework by Exploiting Intrinsic Anatomical Features” paper has been implemented within the AFNI framework. Do you have any tutorial for using it?

Thank you for considering my request!

Hi Reza!
We do have a rat template available. Because of the variability rat MRI and FMRI, I’m not sure there is a specific script, but several approaches can be tried - including ones similar to those in the macaque_align.csh script. Please get in touch with me via email, and we can discuss.

Hi - Any luck with registering rodent fmri > anatomical > template with the AFNI toolset? We’re also interested in this problem!

John & Shahab

The same answer for you. Each scan is so different for rats that it will require looking at your data.