Hello Bianca,
In my invasive work, the electrode information comes from programs separate from the anatomy files. I either import the anatomy in Freesurfer or Brainsuite formats, using Brainstorm’s automatic routines to bring in both the MRI and all of the surfaces in one common coordinate system.
The electrode data, however, come from either an in-house program or the Curry program, as 3-D coordinates hand-selected by a skilled technician. The in-house programs does not have surface renderings nor convenient formats, and we prefer the renderings of Brainsuite and Freesurfer over those of Curry. So we have the need to re-align these electrode coordinates from one coordinate system into the coordinate system Brainstorm assigned to the imports.
To register these coordinates into the Brainstorm anatomy, I extract from the electrode program hundreds or thousands of scalp rendering points, in the same coordinate system as the electrodes. (In Curry, I retrieve their surface rendering of the MRI and downselect 5,000 surface points.) I then create a channel structure identical to Brainstorm’s, but I list the scalp points as additional “head points”.
When I import this channel structure into Brainstorm, it then is easy to use the Brainstorm alignment programs (either “Digitized Head Points” or “MRI Registration”) to align the scalp points of the electrode program with the scalp surface of the anatomy, using a combination of Brainstorm’s manual and automated routines. The electrode information is then naturally aligned with the MRI. Using the MRI viewers, it’s relatively easy to confirm that the registration is the same as was seen in the original electrode program.
Yes, a bit confusing, but we’re merging multiple modalities, instruments, and software here. So I like the approach of getting scalp points in the same coordinates as the electrodes, so I can confirm precise registration.
To mirror Francois’ question, how are you getting electrode information from the Freesurfer folder?
- John