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Do not include the AC/PC/IH points in your file, they are not used for the registration between the MRI and the sensors
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When importing the contact positions, select the file format “EEG: XYZ,Name (.)”. It will ask you to confirm the scaling factor (default value is 0.1, because it expects values in centimeters while you file indicates values in millimeters)
FYI: We improved significantly the tools available in Brainstorm for processing and visualizing SEEG and ECOG data, including new options for volume coregistration. They are now documented in a new tutorial:
http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity