Here is my experience.
For the brain extract, first I usually manually select the brain region slice by slice, and then apply some automatic BET on it.
For the coregister, you can try to manually set some tags in some anatomical regions in each rat, and linear transform them together or into one standard sample.
In my experience, the manually way may takes some time but more reliable.
Let me know, if you need any help.
> On May 19, 2017, at 2:47 AM, Ting Chun Lin <[log in to unmask]> wrote:
> Dear experts,
> I am new to the rat rsfmri analysis, currently I tried to do the pre-processing like brain extract, coregister, however it did not work well. I've searched some previous advices such as multiply the true voxel size by 10 times, use rBET ..... etc.
> I would like to know if anyone can share the experience in rat rsfMRI analysis. Any tips will be help a lot! Even better with the detail parameter setting or analysis pipeline!
> THANKS A LOT AND WISH BEST !!!!