Hi everyone! I have data acquire using a CTF MEG system. I don’t have digitized headshape points, so I need to set NAS/LPA/RPA manually. The subject’s MEG folder contains a .hc file with coil positions, e.g.:
standard nasion coil position relative to dewar (cm):
x = 5.65685
y = 5.65685
z = -27.00000
standard left ear coil position relative to dewar (cm):
x = -5.65685
y = 5.65685
z = -27.00000
standard right ear coil position relative to dewar (cm):
x = 5.65685
y = -5.65685
z = -27.00000
measured nasion coil position relative to dewar (cm):
x = 6.45525
y = 6.50760
z = -21.16790
measured left ear coil position relative to dewar (cm):
x = -4.82564
y = 6.49774
z = -24.60200
measured right ear coil position relative to dewar (cm):
x = 5.64420
y = -4.81848
z = -24.71060
measured nasion coil position relative to head (cm):
x = 8.99161
y = 0.00000
z = 0.00000
measured left ear coil position relative to head (cm):
x = 0.06775
y = 7.70824
z = 0.00000
measured right ear coil position relative to head (cm):
x = -0.06775
y = -7.70824
z = 0.00000
None of these coordinates seem to match Brainstorm’s MRI, SPS, MNI, or World coordinates: inserting them directly misplaces the fiducials.
How should I use these .hc coordinates to set fiducials manually in Brainstorm?
Thanks!
Hello @Francesca27,
There is no need to manually set coordinates for the head coils. When the CTF MEG data is reviewed, the .hc file is read and the positions of the nasion, left ear and right ear coils (relative to the dewar) are used to co-register the MEG helmet (and its sensors) to the Subject anatomy. This is to say, the initial registration is obtained aligning the anatomical fiducials with the head coils.
For sake of completeness, these coordinates are saved in the header.hc field of the Link to raw file file.
If you MRI-MEG registration seems off, it is not possible to refine it using head points, as they are not present in your data. If the co-registration is really off, double-check that the fiducial definition in the MRI corresponds to the places where the head coils were placed.
Check the information in here:
https://neuroimage.usc.edu/brainstorm/CoordinateSystems#Notes_for_CTF_users
In brief, before reviewing the CTF MEG data, set the MRI fiducials in the places where the head coils are on the subject.
- Right-click on the MRI and then Edit... set the NAS, LPA and RPA to match the positions of the head coils during the MEG acquisition.
Thank you Raymundo for your quick response! Actually, that was exactly the point I was trying to clarify. I was wondering where to find the coordinates of the coils used during the acquisition.
Inside Brainstorm, if I go to the Anatomical view, select the raw file, and then check File > View file contents, I can see a file containing the information, including the coordinates of NAS, LPA, and RPA in SCS.. should I use these coordinates for import?
That information is in the .hc file alongside the MEG recordings, and it can be found in Brainstorm in:
These coordinates are not in SCS, these are in cm and are with the coil positions relative to dewar.
In order to co-register your MRI and the MEG, you need two sets of fiducials coordinates:
Set 1: The coil positions relative to the dewar
This are obtained during the MEG acquisition
Set 2: The fiducials positions in the MRI
This should be placed on the MRI, and their locations should correspond to the fiducials in Set 1
With these two sets of fiducials, Brainstorm will (i) create the Subject Coordinate System (SCS) based on the the Set2 fiducial, (ii) align Set1 to Set2 computing a transformation from Set1 to Set2 (SCS), (iii) apply this transformation to all the MEG sensor locations, so the can be in SCS coordinates.
It is not possible to know where to place the fiducials in the MRI (Set 2) from the MEG data, as there are in different coordinate systems.
Hello Francesca,
To rephrase what Raymundo said, in your case coregistration is done by manually marking in the Brainstorm MRI interface, the positions of the head coils *instead* of marking the “real” anatomical fiducials: nasion, LPA, RPA. You need to know where these were placed precisely to achieve a decent coregistration. Taking pictures of the head coils on the participant are essential in this case. Or you can place imaging markers in the same spots as the head coils during the MRI scan, if doing the MRI the same day (vit. E pills is a cheap option for this).
Note that there is a button in the MRI viewer, while editing the fiducials, to view the head surface and current position in 3D to help do this, as it can be difficult placing them precisely in MRI slices.
Note also that this procedure to coregister without head points is not clearly explained in our series of tutorials, but it would happen at the MRI import stage:
Since you need to place the coils on the MRI, it also means it would not be simple to do the coregistration for two different MEG sessions, with slightly different head coil positions, in the same Brainstorm subject. If you have such data, I recommend making different subjects (it can be the same MRI, but import again).
Hi Marc, thanks to you and Raymundo for the clarification.
So if I understand correctly, the only way to get an accurate coregistration in my case would be to have a photo showing exactly where the head coils were placed? And if I don’t have such a photo, the best thing I can do is to manually set the anatomical fiducials when importing the subject’s MRI and continue from there?
That’s partly correct. There’s nothing in the MEG data that can give you coregistration with the MRI. Digitization is one way to help doing it, otherwise you must place the head coils on the MRI, which will be rather imprecise without pictures. Again, in this case you do not want to place the traditional anatomical points, but the head coils.
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