How to run artsBrainExtraction?

pradier · January 12, 2021, 4:34pm

Hello,

I just came across this article on OSF Preprints on brain extraction in rats called artsBrainExtraction. Is there any way I can run this tool on a windows system? As far as I understand I will need nirodents installed.

Best,

Bruno

eilidhmacnicol · January 13, 2021, 1:26pm

Hi Bruno -

Thanks for your interest in artsBrainExtraction!

NiRodents is available as a python package, so it can be used across operating systems. However, we recommend using Docker to ensure the dependencies are available for the toolbox. Please see my previous reply: about how to get started with NiRodents (and artsBrainExtraction) with a docker image.

Otherwise, NiRodents is available via Pypi and can be used with python and is bundled with some shell command-line interfaces for the most common tools.

All the best,
Eilidh