Better cc visualization

[ClePol]

This change only affects the cc visualization script, that is not called in FastSurfer default workflows.

In response to a user request, I improved the "expert script" that has it's own entrpoint.
Most notably

• better documentation
• consistent ordering between script inputs and stats outputs
• dedicated mode to plot p-values on the cc
• added a default fsaverage contour, so users don't have to mount it in manually (also makes the code cleaner)

An example command is

docker run --rm \
    --user "$(id -u):$(id -g)" \
    --volume "$PWD/dummy_p_values.csv:/input/p_values.csv:ro" \
    --volume "$PWD:/output" \
    --entrypoint /fastsurfer/tools/Docker/entrypoint.sh \
    deepmi/fastsurfer:latest \
    python3 /fastsurfer/CorpusCallosum/cc_visualization.py \
    --values_file /input/p_values.csv \
    --output_dir /output \
    --mode p-value \
    --colormap yellow_to_red \
    --log_scale \
    --upper_threshold 0.05 \
    --threshold_color gray \
    --legend "p-value (log scale)" \
    --title "P-values on fsaverage corpus callosum" \
    --output_name dummy_p_values_fsaverage_2d.png \
    --smoothing_window 0 \
    --twoD

[Copilot]

Pull request overview

This PR enhances the CorpusCallosum “expert” visualization tooling by adding a standalone --values_file workflow (e.g., p-values on an fsaverage contour), improving ordering/validation in plotting, and updating documentation to better explain expected input formats.

Changes:

• Added a --values_file mode to cc_visualization.py to plot 1D anterior→posterior value vectors (p-value/icc/thickness) on a bundled fsaverage corpus callosum contour.
• Added CCContour.get_thickness_profile() plus stricter input validation and extended plotting options (log scaling, thresholds, configurable colormap, label overrides).
• Bundled a precomputed fsaverage CC contour (fsaverage_cc_contour.json) and updated docs/README and measure descriptions accordingly.

Reviewed changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Tightens Sphinx argparse dependency constraint for doc builds.
doc/scripts/cc_visualization.rst	Expands usage docs, clarifies thickness file vs profile semantics, adds --values_file examples and figure.
doc/overview/modules/CC.md	Clarifies definitions/formulas for CC metrics and thickness profile description.
CorpusCallosum/utils/types.py	Updates TypedDict docstrings to match clarified metric definitions.
CorpusCallosum/shape/metrics.py	Improves calculate_cc_index docstring and citation, aligns stated defaults.
CorpusCallosum/shape/contour.py	Adds get_thickness_profile() and extends/validates plot_contour_colorfill() (log scale, thresholds, colormap).
CorpusCallosum/README.md	Links to the dedicated CC visualization documentation page.
CorpusCallosum/data/constants.py	Adds a constant path for the bundled fsaverage CC contour JSON.
CorpusCallosum/data/fsaverage_cc_template.py	Switches fsaverage contour loading to a bundled JSON-derived contour.
CorpusCallosum/data/fsaverage_cc_contour.json	Adds the bundled precomputed fsaverage CC contour data.
CorpusCallosum/cc_visualization.py	Adds --values_file entrypoint logic and new CLI options for value plotting.

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[m-reuter]

@ClePol can you reduce the file size of the example png ?

[ClePol]

@ClePol can you reduce the file size of the example png ?

done