[DOC] Add comparison of meaning differences of GLM between different libraries

[tpremrud]

• Closes Add explanations for 1st and 2nd level for glm #2599

Changes proposed in this pull request:

• Added meaning_difference.rst as a documentation file for comparing GLM analysis levels between different libraries (i.e., FSL and SPM)
• Modified the index page of GLM documentation module to include the documentation structure (i.e., drop-down list) for the meaning_difference.rst page.

Note: I am still uncertain if some of the wording and content are redundant (e.g., runs vs sessions, which I am certain are the same, but I included for clarity); please feel free to make any suggestions! :)

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[Remi-Gau]

Thanks for starting this @tpremrud: I can already tell this will be usefull!

Couple of general comments.

I would suggest mentioning that we use the BIDS definitions of "run" in this document (and in general we are trying to move to make this use consistent in nilearn).

Also as far as I can tell all the mentions of the word "session" in your text should be replaced by "run".

https://bids-specification.readthedocs.io/en/latest/common-principles.html#definitions

Run - An uninterrupted repetition of data acquisition that has the same acquisition parameters and task (however events can change from run to run due to different subject response or randomized nature of the stimuli). Run is a synonym of a data acquisition. Note that "uninterrupted" may look different by modality due to the nature of the recording. For example, in MRI or MEG, if a subject leaves the scanner, the acquisition must be restarted. For some types of PET acquisitions, a subject may leave and re-enter the scanner without interrupting the scan.

I do not think we need the whole definition but at least the main bit and then a link to the BIDS glossary:

• https://bids-specification.readthedocs.io/en/latest/glossary.html#run-common_principles

[Remi-Gau]

I suspect that we should mention somewhere that it is typical in the SPM workflow to put all runs in a single design matrix, where as nilearn typically will give you one design matrix per run.

[tpremrud]

Gotcha @Remi-Gau , that's a really great point! However, I'm wondering if I understand the concept correctly, so if there are different conditions, do they still count as a single run if the imaging acquisition is continuous, uninterrupted, and comprise of the same parameters?

I'm looking at nilearn example it seems like there are different conditions within a design matrix, but you said that nilearn gives one design matrix per run, so I'm just not sure if I understand the concept of run correctly as I should or not.

But the SPM really does have a design matrix that goes through all the runs in one matrix.

Thank you!!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.12%. Comparing base (abb80ff) to head (729dd92).
Report is 21 commits behind head on main.

Additional details and impacted files

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