Automatically calculate fiducial point for leadfield

Hi experts,
I am working with leadfield pipeline in individual space.
But the problem is our dataset doesn't contain the fiducial point.
So the only one is manually selecting in the interactive interface?
https://neuroimage.usc.edu/brainstorm/Tutorials/TutRawScript

Can I apply MNI trans and use individual space fiducial point inversed from MNI default fiducial point instead?
Because I don't sure after MNI transform applied, the remaining steps (like calculated head model based on MNI space BEM)will be done in MNI space or individual space? (Because theoretically leadfield should calculate based on individual space BEM).

I tried to read the individual fiducial point from MNI transformed pipeline to do the remaining step. But the results in different with applied MNI transit pipeline( not only in numerical level). So the MNI transform seems influenced BEM surface and compute head model.

Therefore, I need two pipelines for automatically get individual space leadfield? One for applied MNI for getting individual fiducial points another for generating individual space BEM and computer individual head model?

I try my best to describe, but it still looks complicated for understanding. If anything unclear I will attach more information.
Best,
Rigel

https://github.com/rigelfalcon/automatically_fiducial_point_question.git
Here is the two pipeline

Dear Rigel,

If I understand well from your script:

  • this is EEG data
  • you have an MRI for each of your subject
  • but you don't have individual positions for the EEG electrodes and you're planning to use a 10-20 template from Brainstorm.

In this case, I suggest you do the following:

  • After importing the MRI, compute the MNI transformation: this will define a default set of NAS/LPA/RPA points for this subject. It is useless to try to mark accurate anatomical points as you don't have matching accurate points in the same space as the EEG electrodes. Do as illustrated in this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Pre-implantation_MRI
  • Link your EEG recordings to the database
  • Add the EEG electrodes 3D positions from the 10-20 template
  • Right-click on the channel file > MRI registration > Edit, then adjust the positions to the head of your subject: rotations+translations+resize along the three axis (read the tooltips of the various buttons in the toolbar), and finally project the electrodes on the head surface. There is no "truth" we can guess in this procedure, only you know how the electrodes were positions on the head of your participants.

If you had digitized positions for the electrodes, you could use this solution instead:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping

Best wishes,
Francois

Thank you Francois,
Because the EEG electodes 10-20 template is in MNI space and is fitting to MNI space surface, can we just directely inverse the template position back to subjects' individual space? For avoiding manual adjust and making pipeline automatically?
Thank you.
Best,
Rigel

Because the EEG electodes 10-20 template is in MNI space and is fitting to MNI space surface

I thought you were importing the individual MRI of your subjects... I didn't understand correctly then.

If you are using one of the MNI template in Brainstorm, you don't have anything to do. The 10-20 template is already aligned on these templates (at least for Colin27 and ICMB152).

Note that it is probably vain to spend a lot of time trying to be very precise for the EEG source modelling if you are using anatomy templates...

Thank you for your fast reply.
Yes, you were right, I am using individual MRI.
When import template electrode(ICBM152), it derectely overlay on the individual surface(I finished MNI transform, although MNI transforms here not change anatomical data).
Can I project electrode template to individual space?
Thank you.

Which the same transformation as the fiducial point used.
The MNI space to individual space projection.

Then the procedure to align the template electrodes positions on the individual brain is the one I described in the my first message in this thread.


up left: individual head and template electrode in scs system
up right: individual head and template electrode in mni system
bottom left: template head(ICBM 152) and template electrode(BioSemi_128_A1)
bottom right: template head and individual head

Thank you, Francois. Now, I understand, because here we use affine co-registration which is linear transformation, so the shape of the individual head in MNI space is still different from template.
The major part is the back side of head,it may be caused by the fiducial point does not cover information about this part.
Therefore, it still need to adjust electrode position manually.
So can nonlinear co-registration solve this problem here?(to avoid manual adjustment)
Best,
Rigel

Now, I understand, because here we use affine co-registration which is linear transformation, so the shape of the individual head in MNI space is still different from template.
The major part is the back side of head,it may be caused by the fiducial point does not cover information about this part.

The head of your subject and the head surface from the MNI template are different. Different shape, different size. This is not a registration issue, no matter what you do, you will never have them match.

Therefore, it still need to adjust electrode position manually.
So can nonlinear co-registration solve this problem here?(to avoid manual adjustment)

The position of the electrodes on each subject is different. If you don't have the information about the position of the electrode cap on the patient head, I'm sorry there is no nonlinear magic you can do to recover it.
You do have to set manually the position of the cap on the subject head, just like you did when put it on the participants' head before the acquisition. Right-click on the channel file > MRI registration > Edit, then try to place it in a similar way to what you did in real life on the participant. If you have some pictures of the participants with the electrode cap on, it could help.