Installing brainreg


If you know what you're doing just run:
pip install brainreg
If you're not completely sure what you're doing, read on.


The hardware requirements for brainreg depend on the atlas (and in particular the resolution) you want to use. Most machines (including laptops) will be able to use most of the atlases, but some atlases (such as the 10um mouse atlases) may need up to 32GB of RAM.
Currently brainreg works on Windows and Linux.

Setting up your machine

Installing Python

brainreg is written in Python, and so needs a functional Python installation. Your machine may already have Python installed, but I recommend installing miniconda.
See Using conda for details.
brainreg should run on any type of Python installation, but if you don't use conda, I may not be able to help you.

Installing brainreg

Remember to activate your conda environment before doing anything
pip install brainreg[napari]
To only install the command line tool with no GUI (e.g. to run brainreg on an HPC cluster), just run:
pip install brainreg
If you are using macOS then please run "conda install -c conda-forge niftyreg"