Converting SCS coordinates to MNI ones, only having coordinates (no images)?


I'd need to convert some SCS coordinates (based on the Desikan-Killiany atlas) of EEG sources that I found on a paper to MNI coordinates.

I've read a few discussions on how to do this on Brainstorm, but they all assume that I have a file to import into my Brainstorm database, which I don't, since I found the coordinates on a paper. So I'm kind of stuck atm because I don't know how to get my sMri to run the "cs_convert" function...

These the info I have about these coordinates:
(1) left STG (SCS coordinate = [15, 59, 40], vertice number = 290, area = 47.81 cm2);
(2) right STG (SCS coordinate = [23, −59, 37], vertice number = 257, area = 43.98 cm2);
(3) left IFG (SCS coordinate = [40, 56, 60], vertice number = 139, area = 20.90 cm2);
(4) right IFG (SCS coordinate = [43, −57, 62], vertice number = 118, area = 17.05 cm2);
(5) left IPL (SCS coordinate = [−42, 50, 79], vertice number = 351, area = 52.71 cm2);
(6) right IPL (SCS coordinate = [−36, −50, 82], vertice number = 421, area = 61.33 cm2)

Any help would be greatly appreciated :slight_smile:

Thanks in advance :slight_smile:

As it name specifies, the (Subject Coordinate System) SCS depends on the Subject anatomy.

So, the same SCS coordinates will point to different parts of the brain for different subjects. As such, the Subject anatomy is required to convert to MNI coordinates.

If the article in question (1) used Brainstorm, (2) mentions that a default anatomy was used, and (3) also indicates which default anatomy was used. Then it could be possible to import the same default anatomy and check the MNI coordinates. If the article reports on the subject's anatomy, you need the MRI.

Right indeed makes sense.. :slight_smile: In the paper they say:

An overlapping‐sphere method was used to resolve the forward problem. The cortically constrained source imaging was subsequently performed by means of depth‐weighted minimum norm estimate (MNE) over a set of ~15,000 dipoles distributed on the cortex.41 The individual's MNE map was then rescaled to fit the previously defined head points, with the default parameter settings in the brainstorm software.42 The MNE maps of MMNm from each group were averaged onto the ICBM152 brain template for further analysis.

So they used the ICBM152 brain template, which is the first in the BrainStorm list:

I opened it, and then right clicked and exported it to Matlab as sMri. I checked that sMri was not empty and the export seemed to be successful but when I run the cs_convert function with the command

P_mni = cs_convert(sMri, 'scs', 'mni', P_scs)

despite not giving error, it outputs an empty P_mni matrix..

Any ideas on why this could be the case? Am I using running the function with wrong arguments or something?

Thanks a lot for your answer :slight_smile:

This sentence indicates that the default anatomy was not use for each of the subjects, but a warped version of the default anatomy. However, I guess the reported SCS coordinates correspond to the ICBM152 that was used. It will be helpful if you post the link to the article.

There are different versions of the ICBM152 while it is the same MRI, it has been pre-processed with different versions of FreeSurfer, and more atlases have been added with the time. After an inspection, it seems the one used in the article was the ICBM152_2019.

Those are the correct arguments and the correct steps: Export the MRI (iconMri) to Matlab as sMri and

P_mni = cs_convert(sMri, 'scs', 'mni', P_scs)

P_scs is size [nPoints, 3] and must be given in meters.

Thanks again for your answer!

The article I was referring to is this one: Altered mismatch response of inferior parietal lobule in amnestic mild cognitive impairment: A magnetoencephalographic study - PMC

In the list of templates, I can only find ICBM152 2023b and I can't find ICBM152_2019 online either: could you send me the link to download ICBM152_2019? --> Sorry, I solved thanks..

And for the command I solved indeed by running it on one row at a time P_mni = cs_convert(sMri, 'scs', 'mni', P_scs(1,:)) --> So SCS coordinates are in mm too and need to be converted to m?

Thanks again :slight_smile:

Right click on the Default anatomy > Use template > MNI > ICBM152_2019

Yes, the need to be converted to meters before using cs_convert() and the result coordinates in MNI are also in meters