Question about macaque_align.csh in macaqueatlas_1.2a?

Hi all!

I am creating macaque topology using macaque_align.csh.
In the README_AFNI.txt of macaqueatlas_1.2a, there is an example as below.

EX: tcsh -x …/macaque_align.csh macaque1+orig …/…/D99_template.nii.gz
…/…/D99_atlas_1.2a.nii.gz …/…/D99_atlas_1.2a_right.nii.gz | & tee test1.log

We are calculating only right. Do you have to calculate the left side separately after the right side calculation is done?

Thank you in advance to whomever can help! I’m pretty new, so any advice will help.


The script will transform the segmentation for the whole macaque brain and for a selected hemisphere separately too. You don’t have to include the left or right side as a separate step at all and just use the whole brain segmentation. This was provided as a convenience for surface visualization, but you can do this manually outside of the script.