[ENH, MRG] Add coregistration video and execute GUI in tutorial to show window & add show and block to GUIs

[alexrockhill]

Fixes #9451, fixes #10801.

[alexrockhill]

Alright! A bit of the code is a tiny bit inelegant but that will be fixed with future PRs that slightly refactor the window classes so that they don't depend on the 3D renderer, harmonizing between the coreg & brain GUIs and the ieeg_locate GUI. For now, I think this is great, the video looks good and the GUI is scraped and appears in the docs, real progress I think https://output.circle-artifacts.com/output/job/754bf05f-35bd-4deb-8050-67f788191330/artifacts/0/dev/auto_tutorials/forward/20_source_alignment.html.

[agramfort]

@alexrockhill in the video you pick the fiducials too high. In this subject the LPA and RPA should be just just below the targus

[alexrockhill]

@alexrockhill in the video you pick the fiducials too high. In this subject the LPA and RPA should be just just below the targus

Ok, I will reshoot picking as in here https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/

[alexrockhill]

Ok new video is up, looks good https://output.circle-artifacts.com/output/job/a249d7a8-3e0b-4508-9864-8bca3bc5fa25/artifacts/0/dev/auto_tutorials/forward/20_source_alignment.html#defining-the-headmri-trans-using-the-gui. I did notice that there was a reference to toggling head points that is defunct so I'll fix that.

[alexrockhill]

I noticed that the text instructions were out-of-date so this fixes those as well.

[agramfort]

nice ! 2 nitpicks: - you can use omit button after the first ICP fit to remove the outlier point - the scaling option is more if you have an individual digitization (aka the head shape points) but you don't have the MRI. You use then the dig points as proxy for the head size etc. Message ID: ***@***.***>

…

[alexrockhill]

Ok, I'll give the video one more shot

[alexrockhill]

@agramfort, if you have time for one more look, sorry for the bad takes, you can playback at double speed and it's only two minutes 😄 https://youtu.be/ALV5qqMHLlQ

[cbrnr]

Maybe something for the text (I don't want you to redo the video again), but I have been wondering where the exact location of a fiducial marker actually is. Is it at some vertex? Or the center of mass inside the shape? Probably worth mentioning because that shape has a non-negligible shape.

[alexrockhill]

I was going off https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/ @cbrnr, we could link that in the tutorial

[cbrnr]

No, I meant which point in that fiducial marker (two stacked pyramids) is the origin? Should I use the top vertex or the bottom one to set the fiducial location?

[alexrockhill]

I think it's the center of mass of the shape... does that help?

[cbrnr]

Sure! We should mention this.

[alexrockhill]

@cbrnr, I added that info in the text

[agramfort]

video is great !

are all the changes in this PR related? I see you touch stuff in GUI code and I want to know how deeply I need to review this

[alexrockhill]

If you could give it 5 minutes that would be really helpful but I'm not too worried about things breaking since I'm mostly just using things that have worked in the other GUI for the coreg and ieeg_locate GUIs to harmonize. I abstracted the scraper to work for the coreg GUI as well so that it could be displayed inline and then I added show and block so that it wouldn't block the execution in the tutorial. Those are so that the code actually executes in the tutorial which I think is really important for maintenance. I added show and block to the ieeg_locate GUI while I was at it for symmetry. All of those are pretty minor changes, I'm not too worried about them breaking because they worked on the other GUI and I'm just harmonizing. Lastly, I fixed the wording suggesting that you could only launch coreg from the CLI which I think is a bit out-of-date per @hoechenberger 's issue.

[larsoner]

@agramfort is happy with the video, I'm happy with the code, and I don't see any unresolved comments so in it goes, thanks @alexrockhill !