1. Run: ct2mriBbreg.sh
2. When ct2mriBbreg.sh is done, it will give you a tkregister2 command that will allow you to check the coregistration results. It will look something like this:
tkregister2 --mov /Users/WilderPenfield/Downloads/Users/WilderPenfield/Desktop/PT048/elec_recon/Gap_Corrected_Axial_Axial_Axial_Head_2_000_s007.nii.gz --reg /Applications/freesurfer/subjects/PT048postEx/elec_recon/ct2mri.dat --surf
 
Note, newer versions of FreeSurfer will give a command that is analogous to the command above, but it calls the FreeView-based version of tkregister. If it doesn't work, you can just use tkregister2.
 
3. When using the tkregister2 GUI to manually adjust the CT scan orientation, we recommend ONLY translating and rotating the CT scan. You probably shouldn't need to scale it and accidentally scaling the different dimensions of the CT scan to different degrees will deform the head.
4. Save the manually adjusted registration to disk as ct2mri.dat. This will overwrite the existing ct2mri.dat.
5. Run the iELVis script ct2mriManual.sh