CorpusCallosum: cc_visualization.py
===================================

.. argparse::
   :module: CorpusCallosum.cc_visualization
   :func: make_parser
   :prog: cc_visualization.py

Usage Examples
--------------

3D Visualization
~~~~~~~~~~~~~~~~

To visualize a 3D template generated by ``fastsurfer_cc.py`` (using ``--slice_selection all --save_template_dir ...``),
point the script to the exported template directory:

.. code-block:: bash

    python3 cc_visualization.py \
        --template_dir /data/templates/sub001/cc_template \
        --output_dir /data/visualizations/sub001

2D Visualization
~~~~~~~~~~~~~~~~

To visualize a 2D template (using ``--slice_selection middle --save_template_dir ...``):

.. code-block:: bash

    python3 cc_visualization.py \
        --template_dir /data/templates/sub001/cc_template \
        --output_dir /data/visualizations/sub001 \
        --twoD

.. note::

   The ``--template_dir`` is the required way to load the templates
   produced by ``fastsurfer_cc.py``.

Outputs
-------

3D Mode Outputs (default):
    - ``cc_mesh.vtk``: VTK format mesh file for 3D visualization
    - ``cc_mesh.fssurf``: FreeSurfer surface format
    - ``cc_mesh_overlay.curv``: FreeSurfer overlay file with thickness values
    - ``cc_mesh.html``: Interactive 3D mesh visualization
    - ``cc_mesh_snap.png``: Snapshot image of the 3D mesh
    - ``midslice_2d.png``: 2D visualization of the middle slice

2D Mode Outputs (when ``--twoD`` is specified):
    - ``cc_thickness_2d.png``: 2D contour visualization with thickness colormap