unravel.cluster_stats.sunburst module#

Use cstats_sunburst from UNRAVEL to generate a sunburst plot of regional volumes across all levels of the ABA hierarchy.

Prereqs:

  • cstats_summary generates a valid rev_cluster_index.nii.gz (clusters of significant voxels) via cstats_index.

Inputs:

  • path/rev_cluster_index.nii.gz (e.g., with valid clusters), path/labeled_image.nii.gz, or path/binary_image.nii.gz

  • path/atlas.nii.gz (Default: atlas/atlas_CCFv3_2020_30um.nii.gz) for applying region IDs to the input image

Outputs:

  • path/input_sunburst.csv and [input_path/sunburst_RGBs.csv]

Note

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

  • Region info csv: CCFv3-2020_info.csv (or use CCFv3-2017_info.csv or provide a custom CSV with the same columns)

Next steps:

  • Use input_sunburst.csv to make a sunburst plot or regional volumes in Flourish Studio (https://app.flourish.studio/)

  • It can be pasted into the Data tab (categories columns = Depth_`*` columns, Size by = Volumes column)

  • Preview tab: Hierarchy -> Depth to 10, Colors -> paste RGB codes from sunburst_RGBs.csv into Custom overrides

Usage:#

cstats_sunburst -i path/rev_cluster_index.nii.gz [-a atlas/atlas_CCFv3_2020_30um.nii.gz] [-rgb] [-scsv sunburst_IDPath_Abbrv.csv] [-icsv CCFv3-2020_info.csv] [-v]

unravel.cluster_stats.sunburst.parse_args()[source]#
unravel.cluster_stats.sunburst.calculate_regional_volumes(img, atlas, atlas_res_in_um)[source]#

Calculate the volumes of labeled regions in the input image.

Parameters:

  • img (-) – the input image ndarray.

  • atlas (-) – the atlas ndarray.

  • atlas_res_in_um (-) – the atlas resolution in in microns.

Returns:

a dictionary of region volumes (key = region ID, value = volume in mm^3)

Return type:

  • volumes_dict (dict)

unravel.cluster_stats.sunburst.sunburst(img, atlas, atlas_res_in_um, output_path, sunburst_csv_path='sunburst_IDPath_Abbrv.csv', info_csv_path='CCFv3-2020_info.csv', output_rgb_lut=False)[source]#

Generate a sunburst plot of regional volumes that cluster comprise across the ABA hierarchy.

Parameters:

  • img (-)

  • atlas (-)

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

  • output_rgb_lut (-) – flag to output the RGB values for each abbreviation to a CSV file

Outputs:

  • CSV file containing the regional volumes for the sunburst plot (input_sunburst.csv)

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