findAllenConnectome Finds connectivity data between two brain regions

Syntax

filename = findAllenConnectome(sourceId, targetId, sourceHemi, targetHemi)
[filename, sourceMask, targetMask] = findAllenConnectome(___)

Description

filename = findAllenConnectome(sourceId, targetId, sourceHemi, targetHemi) finds the filename for connectivity data between two specified brain regions in the Allen Mouse Brain Atlas, after it has been downloaded from python.

[filename, sourceMask, targetMask] = findAllenConnectome(_) also returns binary masks for the source and target brain regions at a fixed resolution of 100 microns.

Input Arguments

sourceId - ID of the source brain region (integer)

targetId - ID of the target brain region (integer)

sourceHemi - Hemisphere of the source region (1 = Left, 2 = Right, 3 = Both)

targetHemi - Hemisphere of the target region (1 = Left, 2 = Right, 3 = Both)

Output Arguments

filename - Full path to the connectivity data file (character vector)

sourceMask - Mask for the source brain region (logical array)

targetMask - Mask for the target brain region (logical array)

Usage Notes

The resolution of the connectivity data is fixed at 100 microns.

Authors

Mehul Gajwani, Monash University, 2025