[DOC] Improve tutorials for generating `-trans.fif`

In the process of setting up a source-space-analysis, it took me a really long time to realize all the steps necessary to create a -trans.fif. As I am new to these type of analyses, it could be just me not knowing the terminology and what to look for, but I think there could be a more intuitive description of the procedure here.

Specifically, I needed several readings of the tutorials and attempts in implementing to figure out these things:

• if I haven’t created a -trans.fifmyself or use an existing data set for which someone else has created that file, I will have to run mne coreg (i.e. the phrasing in the tutorials implies that normally this file is present, and only in the exceptional case that it is not, I need to take actions. So, it looked for it in different places, and tried to find out how I could extract it)
• getting the head shapes/surfaces with BEM or with make_scalp_surfaces is a prerequisite for running mne coreg
• to obtain the trans.fif I first need to complete other analysis steps (i.e. FS segmentation, BEM)

Proposed documentation enhancement

I don’t know what would make the most sense. Relevant doc regarding the trans.fif file can be found in these two tutorials:

• https://mne.tools/stable/overview/cookbook.html#anatomical-information
• https://mne.tools/stable/auto_tutorials/source-modeling/plot_source_alignment.html#plot-source-alignment

The procedure to run mne coreg is currently buried quite deep in the Source alignment tutorial, which is primarily about understanding all the relevant coordinate systems. Perhaps it would make sense to split the tutorial in two? Or add the part Defining the head↔MRI trans using the GUI to “The typical M/EEG workflow” when talking about the trans.fif file?

Also, the figure in the “The typical M/EEG workflow” tutorial is misleading in that it implies getting the MRI-head trans does not depend on any other analysis step before. That is not true as you need Freesurfer to run its segmentation and to set up a BEM model (afaik, at least). So, I think the figure should be adapted to reflect that, and maybe some textual changes in the tutorial could clarify the dependencies.

[vagechirkov]

Regarding the -trans.fif file generation this tutorial from NiBabel was very useful to me.

[larsoner]

Bumping the milestone on this one, but if someone is motivated to fix/update the docs in the next week or so it could still make it into 0.24