unravel.cluster_stats.index module#

Use cstats_index (ci) from UNRAVEL to create a cluster index with valid clusters from a given NIfTI image.

Outputs:

  • path/valid_clusters/rev_cluster_index_valid_clusters.nii.gz

  • path/valid_clusters/cluster_``*``_sunburst.csv

Note

  • Default csv: UNRAVEL/unravel/core/csvs/sunburst_IDPath_Abbrv.csv

  • CCFv3-2020_info.csv or CCFv3-2017_info.csv

Usage#

cstats_index -i path/rev_cluster_index.nii.gz -ids 1 2 3 [-a atlas/atlas_CCFv3_2020_30um.nii.gz] [-vcd valid_clusters_dir] [-rgb] [-scsv sunburst_IDPath_Abbrv.csv] [-in CCFv3-2020_info.csv] [-v]

unravel.cluster_stats.index.parse_args()[source]#
unravel.cluster_stats.index.generate_sunburst(cluster, img, atlas, xyz_res_in_um, data_type, output_dir, sunburst_csv_path, info_csv_path, output_rgb_lut)[source]#

Generate a sunburst plot for a given cluster.

Parameters:

  • cluster (-) – the cluster ID.

  • img (-) – the input image ndarray.

  • atlas (-) – the atlas ndarray.

  • atlas_res_in_um (-) – the atlas resolution in microns. For example, (25, 25, 25)

  • data_type (-) – the data type of the image.

  • output_dir (-) – the output directory.

unravel.cluster_stats.index.main()[source]#