Fix plot_approach_figures execution during book build

[eurunuela]

Problem

content/plot_approach_figures.md fails to execute during the Jupyter Book build. There were two execution-halting bugs in the chapter:

1. The setup cell referenced func_dir without defining it → NameError: name 'func_dir' is not defined (the originally-reported failure).
2. After fixing that, the "Prepare data for model" cell ran -1 * data['echo_times'] on the list returned by load_pafin (-1 * a_list yields []), raising ValueError in np.column_stack.

The cell also builds a background anatomical image from a boldref->T1w transform that the data-download step never fetches (a git-annex file), so it would fail wherever that file is absent.

Changes (content/plot_approach_figures.md only)

• Define func_dir in the setup cell (data/ds006185/sub-24053/ses-1/func/), matching 04_Dual_Echo_Denoising.md and load_pafin. ted_dir was already correct.
• Coerce echo_times to a NumPy array once after load_pafin, so the chapter's array arithmetic works. Kept local to this chapter — load_pafin still returns a list, which 02/03 rely on.
• Guard the bg_img construction: fall back to nilearn's default background (bg_img=None, a documented mode) when the boldref->T1w transform or the T1w image are absent.

Verification

• Executed the full page via nbclient (which raises on any cell error — this is what caught the echo_times bug): all 38 cells run clean.
• UV_PROJECT_ENVIRONMENT=meda uv run --locked jupyter-book build ./ re-executes the page (77.9 s) and emits all 16 figures (including the bg_img=None adaptive-mask figure); build succeeded.

Out of scope / note

The chapter's tedana-derivative loads remain unguarded — they rely on data/tedana being present (generated by chapter 03, which persists across builds since make clean spares data/). Because this chapter is ordered before 03 in the TOC, a clean-data build would still render it broken. Reordering it after 03 would fix that, but is left out here (the chapter is also slated to be merged into TE_Dependence/Signal_Decay).

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Fixes execution failures in the Jupyter Book build for content/plot_approach_figures.md by aligning the chapter’s setup with load_pafin output types and making background-anatomy handling robust when optional dataset files are missing.

Changes:

• Define func_dir in the setup cell to avoid a NameError.
• Convert data["echo_times"] from list to np.ndarray to ensure downstream array arithmetic behaves correctly.
• Make bg_img optional by only constructing it when both the boldref→T1w transform and T1w file are present; otherwise use bg_img=None.

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[tsalo]

I think the download step should fetch these instead of making the later code more flexible.

[eurunuela]

Good call — done in 1a0bd21. The download step (00_Download_Data.md) now datalad gets the boldref→T1w transform and the T1w image, and the bg_img block is back to its original unconditional form (the func_dir / echo_times fixes stay). Verified the chapter executes end-to-end with the fetched files.