unravel.cluster_stats.index module#
Use cstats_index 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 -ci 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.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.