I actually generated the batch using the GUI of SPM and ask it to generate the Matlab script.
Good! I added the option to run the SPM Segment batch with 2 channels T1+T2.
If there is a file with the tag "t2" in its comment in the subject, the GUI would ask whether you want to use it in the computation. For the process version, I added an option "Use T2 when available".
Thanks for the suggestion.
Can you please try it and let me know if it works with your files?
Especially, I saw that the output T2 of free surfer is cut to contains only the brain (eg no eye or skull)
For what I understood, the T2 is mostly useful to refine the cortical surface.
For the T1 and T2, I guess I should import them in brainstorm and then register and reslice the T2 to the T1 image;
I don't know whether the T2 should be resliced on the T2 for the various segmentation methods. This might result in a loss of resolution...
@tmedani?
For the the SPM Segment: maybe you can try this yourself (whether you need to coregister T1+T2 first, or whether SPM does this coregistration anyway when there are multiple channels)?