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.
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