you should go step by step – if the registration is not good, Lead-DBS will not find the electrode.
We need a bit more info to really help you. You could also check out our Slack channel where you could easily send us some screenshots (See Help/Support above).
It’s not so easy anymore to do normalizations manually, but you could easily perform coregistrations (e.g. post-
to pre or between multiple pre images) manually somewhere else.
In case of post-op CT, you’d need to call the registered CT “rpostop_ct.nii”, in case of postop MRI just call it postop_tra.nii. If you have multiple postop MRIs, you could call them postop_tra.nii and postop_cor.nii, postop_sag.nii.
If all your acquisitions are manually co-registered, just choose “already coregistered” during normalization.
Re normalization, I’d recommend to start with ANTs which seems most robust.
Hope this helps, Andy