If you script your analysis, you can use the process "Import > Import anatomy > Compute MNI transformation" (equivalent of clicking on the button with the same name in the MRI Viewer).
This computes a 4x4 affine transformation to register the subject brain to the MNI template (ICBM152). If the anatomical fiducials (NAS/LPA/RPA) are not defined yet, this process also projects the default positions for these fiducials from the template to the subject anatomy.
Therefore yes, these points can be set automatically, at least approximately.
The problem is: how do you register the anatomy with the sensor positions?
- If you use a head shape coming from a 3D scanner (eg. Polhemus), and have the file that includes the NAS/LPA/RPA: you can't use the default positions in the MRI, you need to set them manually and accurately.
- With EEG, if you use a template position for the EEG electrodes: you still need to manually re-align + project on the scalp the electrode.
Only the studies with no individual anatomical information (EEG with anatomy template + default electrode positions) can be ran fully automatically.
You can find various examples in the scripts corresponding to the tutorials in the section "Other analysis scenarios" (brainstorm3/toolbox/script/tutorial_*.m)