clabtoolkit v0.6.1

Highlights

• Sample data from Zenodo. The sample data (the Colin27 average brain in the tallin space) is now published in a Zenodo record (10.5281/zenodo.23702131). The new misctools functions list_sample_data, fetch_sample_data and get_sample_data_dir download the surfaces, cortical maps and tractograms the first time they are needed, check them against their SHA-256 checksums and cache them (set CLABTOOLKIT_DATA_DIR to use another folder). The annotations, the parcellation and the transform are shipped with the package. pooch is now a dependency.
• Notebooks, quickstart and README use the retrieved data. They no longer need FreeSurfer outputs, and simulation is kept only for data the sample set lacks, such as functional images. The new notebook examples-representative-workflows.ipynb contains three end-to-end workflows.
• New surface formats. Surface.load_from_file reads GIFTI, VTK, PLY, OBJ and STL surfaces, Surface.save_surface exports GIFTI, and Surface.load_scalar_maps reads GIFTI shape maps. compute_reg_val_fromannot also reads GIFTI maps.
• New tractogram and points methods. Tractogram.remove_maps removes maps and their colortables, and PointsCloud.to_surface converts points to a surface of spheres.
• Connectome plots. Connectome.plot_matrix has new save_path, dpi and overwrite options, and a groups option that orders, separates and labels the regions by group.

Changes that may affect your code

• PointCloud is now PointsCloud, merge_pointclouds is now merge_pointsclouds and its pointclouds parameter is now pclouds. The old names are not kept as aliases.
• AnnotParcellation.export_to_tsv gives the index 0 to the unknown regions from 1.
• data/parcellationtools is now data/parcellations. The sample subject is sub-colin27, the file names follow the BIDS entity order, and the annotations are .label.gii files.
  The sample surfaces, cortical maps and tractograms are no longer inside the p

Documentation

• New docs cards for the representative workflows and for `clabtoolkit_exampl
• The table of contents of the usage notebooks links to the headings, so it works in the VS Code outline, and typos were corrected.

Full details are in HISTORY.rst.