Hello;
i will soon start to reorganize some of my data in BIDS format and i was having some question on the coordinate system to use.
I have the coordinate of the electrodes outsides brainstorm coming from our digitalization system in SCS coordinate (based on Nasion/left, and right ear) + headpoints and also inside Brainstorm after the co-registration with the MRI (using headpoints to refine the coregistration).
If i want to share the data in BIDS, which coordinate should I export ?
Regards,
Edouard
If you have access to the anatomy of the subjects: I think that the least ambiguous solution for saving anatomical coordinates in BIDS is to link them to the scanner coordinates of the T1w image of the subject, ScanRAS. Make sure you set the IntendedFor correctly in the space-ScanRAS_coordsystem.json file.
https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html#ieeg-specific-coordinate-systems
This does not require to rely on any additional anatomical landmark, and I think most programs now handle correctly the QFORM/SFORM matrices of the .nii files. This requires however the t1w.nii file to be correctly formatted: with only the QFORM matrix with qform_code=NIFTI_XFORM_SCANNER_ANAT, and no SFORM - to avoid ambiguities.
This corresponds to "world" coordinates in Brainstorm, if the reference MRI of the subject in the Brainstorm database is the t1w.nii of the BIDS dataset (and NOT the FreeSurfer-processed version of it, for instance).
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#World_coordinates
You could also use the CTF coordinate system, but as this is not defined for EEG explicitly, some programs might not interpret this correctly. And it requires the simultaneous definition of LPA/RPA/NAS, which is another step source of possible misinterpretation.
You can also export the coordinates in multiple coordinate systems, to increase the chances of having at least one interpreted correctly in all the programs. This is what I did in some iEEG BIDS examples, defining both a T1-based referential and SPM-MNI coordinates:
https://github.com/bids-standard/bids-examples/tree/master/ieeg_epilepsy_ecog/sub-ecog01/ses-postimp/ieeg