unravel.cluster_stats.brain_model module

Use cstats_brain_model (cbm) from UNRAVEL to prep an img.nii.gz and RGBA.txt LUT for vizualization in dsi_studio.

Prereqs:

• Use cstats_summary or cstats_index to generate a valid cluster index.

Inputs:

• input.nii.gz (e.g., a valid cluster index, but can be any binary or labeled image)

Outputs:

• img_ABA.nii.gz (Allen brain atlas labels were applied) or img_ABA_WB.nii.gz if -m was used (WB = Whole Brain)

• rgba.txt (RGBA values for each region in the cluster index)

Note

• The input image will be binarized and multiplied by the split atlas to apply region IDs.

• Split means the left hemisphere region IDs are increased by 20000.

• CCFv3-2020_regional_summary.csv is in UNRAVEL/unravel/core/csvs/

• It has columns: Region_ID, ID_Path, Region, Abbr, General_Region, R, G, B

• Alternatively, use CCFv3-2017_regional_summary.csv or provide a custom CSV with the same columns.

Next steps:

• Use DSI Studio to visualize img_WB.nii.gz with the RGBA values.

Usage:

cstats_brain_model -i input.nii.gz [-m] [-ax 2] [-s 0] [-sa atlas/atlas_CCFv3_2020_30um_split.nii.gz] [-csv CCFv3-2020_regional_summary.csv] [-v]

unravel.cluster_stats.brain_model.parse_args()

unravel.cluster_stats.brain_model.main()