Edit MRI Question

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1

Hi Brainstorm community,

I was experimenting with source mapping today in what I would call "practice_protocol" before I analyse real experimental data and found something that I haven't seen before.

The first time this happened I couldn't document how or why it happened (but it did happen while I was in the "practice_protocol"). I do know that I had "MRI segmentation > Generate BEM surfaces > Brainstorm" loaded in anatomy and that I had both the 3-shell sphere head model and openMEEG head model already loaded into the "practice_protocol".

Anyways, I tried to get the same message by experimenting more and it usually happens on a new protocol where source mapping has not been done before. Here is what I know so far...

Once I right-clicked on a recording to do "compute head model" the following window came up.
I did NOT click YES - I either clicked "NO" or the "X" button to escape from the window as I did NOT wish to edit the MRI orientation (I am using default MRI for everything).
edit MRI

Once I clicked "NO" or the "X" button to escape from the above window I got the below window.
default MRI

Regardless of whether you click "OK" or "X" in this situation and exit the corresponding MRI window, you get the following window. If you then try to "compute head model" again the same window also appears.
image

So now, my question is If you only use standard anatomy (no access to individual MRI) and different positions were not used at all at any acquisition is it still necessary to check and fix the fiducial positions?
I wish to do this right before going into real experimental data.

Additionally, I notice a discrepancy in "default anatomy" between my newer protocols (LEFT) vs my older protocols (RIGHT). Shown below side by side.

What are the reasons for this?

And will there be issues due to the difference between "MRI: ICBM152 2023b" VS "MRI: ICBM152"?

image
image545×743 76.2 KB

2

I'm trying to guess what happened...
for me, it seems that you have changed/edited the MRI fiducial points.
so if you compute again a new head model it will be different from the previous one that you computed since the fiducial points are changed, therefore the chance to have the electrode moved too.

This warning appears only in specific cases while some results are already computed, then some changes are introduced to the anatomy or channels.

if you start a new protocol without editing the files, you will not get this message.

as stated in the name, 2023 is the new release of the ICBM head model.
You can still get the previous model as well using ==> Right-click on the Default anatomy node, then Use template and select the desired template.

3

Thanks for the answer :slight_smile:

Still... If you only use standard anatomy (no access to individual MRI) and different positions were not used at all at any acquisition is it still necessary to check and fix the fiducial positions?

4

No, if you use the default anatomy, it will use it as the default MRI, and the fiducial points are already computed.
For the channel, you can load the template as well, and they should be already aligned to the template, so you do not need to change the fiducials.

5

wonderful! thank you very much :smile:

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