Hi Brainstorm team,
I’d like to perform a source model from an EGI 256 net using the individual MRI anatomy, but I had some problems co-registrating the digitizer file (.sfp) and individual MRI, partially solved reading past threads in the forum.
I’m still in doubt about the rules for importing Digitizer file in Brainstorm.
The Digitizer file (.sfp) contains 259 lines – 256 electrodes (1,2,3…255,256), N, A1, and A2, last three renamed with Wordpad respectively nas, lpa and rpa.
Brainstorm seems not to recognize NAS fiducial point.
I tried to modify .sfp digitizer file, leaving only the 3 fiducial points (nas, lpa and rpa).
lpa 55.0879 -16.5162 -5.97084
rpa -75.4777 -8.47449 4.47727
nas -4.91537 -81.1192 44.0722
When I work on "Digitized head points" and I try to “add points”, BS adds two head points (lpa, rpa), ignoring “nas” (I can realize viewing head points on individual Head).
The coregistration with all electrodes turns out quite good, but I think that it could be even better with a fiducial point (nas) more.
Have you any idea what could be the problem?
Last obvious question: when I import the channel file, have I to answer “yes” to this question?
“There is a transformation to subject coordinates available in the MRI. Would you like to use it to align the sensors with the MRI?”
Thank you kindly in advance!
Matteo
Hi Matteo,
The correct procedure is partly documented in the "EEG & Epilepsy" tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Prepare_the_channel_file
- Link your recordings to the database
- Right-click on the channel file > Add EEG positions, then make sure you select the correct file format in the import dialog window
- This will load the electrodes positions and register them to the Brainstorm coordinates system (SCS: https://neuroimage.usc.edu/brainstorm/CoordinateSystems) using the 3 fiducials also present in the file. After this registration is done, the fiducials don't need to be kept, this is why you don't see them anywhere, but if you see a OK alignment after loading the positions, it is that they have used. You should not have to load this file a second time or use any of the options available in the menus "Digitized head points".
Last obvious question: when I import the channel file, have I to answer “yes” to this question?
“There is a transformation to subject coordinates available in the MRI. Would you like to use it to align the sensors with the MRI?”
This is something that is also mentioned in the EEG tutorial. If you have the NAS/LPA/RPA points available in your .sfp file, you don't need to use the MRI voxel>world transformation. Answer NO here, and Brainstorm will already have all the information it needs for importing your file correctly.
renamed with Wordpad respectively nas, lpa and rpa.
How were this points called initially?
Brainstorm already detects a large number of fiducial names automatically ('nas', 'nasion', 'nz', 'fidnas', 'fidnz', 'lpa', 'pal', 'og', 'left', 'fidt9', 'leftear', 'rpa', 'par', 'od', 'right', 'fidt10', 'rightear'), so you might not need to rename them explicitly.
Cheers,
Francois
Hi Francois,
thank you very much for the answer, thank to your explanations, now coregistration is fine.
The points were called initially A1 (lpa), A2(rpa) and N (nas).
Many thanks,
Matteo
