afni.nimh.nih.gov

Thank you both so much for the help.

I tried both approaches although using @Align Centers (etc...) seemed to get the alignment closer.

When trying to open the myclusters_MNI.nii.gz, the clusters will not open on the MNI_T1_2009 template. Instead, the S_template_3.nii.gz automatically opens as the underlay.

I tried 3drefit -view tlrc -space MNI myclusters_MNI.nii.gz to see if that might fix it, but it did not.

I also tried everything listed above and reorienting the original cluster map (myclusters.nii.gz) to lpi to match MNI_T1_2009 template before running any commands. Originally, myclusters.nii.gz is in lai.

Attached is the picture I have of myclusters_MNI.nii.gz on S_template_3.nii.gz

Any suggestions on how I could keep troubleshooting?

I will also look into the coordinates suggestion as well, although for visualization am hoping for a figure on the MNI brain.