Script to download and prepare connectivity data from the Allen Mouse Brain data portal ABI-connectivity [1]. This script will query the database, download available data, convert it from the nrrd format to NIfTI, and register it to a standard space (DSURQEC, as seen in the relevant mouse brain preprocessing article).
Current recommended release in bold typeface:
- ABI-connectivity-data-0.2.tar.xz [SHA512 checksum]
- ABI-connectivity-data-0.1.tar.xz [SHA512 checksum]
Citation guidelines for use of the Allen mouse brain atlas can be found at: https://alleninstitute.org/legal/citation-policy/
In order to create a new version of the ABI-connectivity data package, simply navigate to the root directory of this repository and run:
python abi_connectivity.py -v 0.5 -x 200
This will create the archive with the newest files at 200um resolution fetched from upstream and processed according to the instructions standardized in this package.
The version suffix will be 0.5 (as per the -v 0.5 parameter).
To create the ABI-connectivity-dataHD archives, run:
python abi_connectivity.py -v 0.5 -x 40
This will create the archives with the newest files at 40um resolution.