Hi Bruno -
My name is Eilidh, and I am one of the team working on fmriprep-rodents and NiRodents.
These are technically two separate (but overlapping) projects; NiRodents is a toolbox for rodent image processing, which contains
artsBrainExtraction, our brain masking tool. On the other hand, we intend for fmriprep-rodents to be similar to the original fMRIprep, in that it will automate the processing of rodent MRI images using many different tools, including those available in NiRodents.
To answer your questions: NiRodents is currently functional, and we encourage people to help us test it out! fmriprep-rodents is currently a work-in-progress, but we hope that it will be available for wider testing very, very soon.
To run NiRodents on a windows system, we recommend using Docker and pulling the latest image from
nipreps/nirodents. The default entrypoint of the docker image is to run
artsBrainExtraction by default, using a command like:
docker run --rm -it -v /path/to/data:/data:ro -v /path/to/output:/out -v /path/to/templateflowcache:/templateflow -e TEMPLATEFLOW_HOME=/templateflow nipreps/nirodents:latest /data/sub-01_T2w.nii.gz -o /out/
or alternatively, running the tool from the bash command within the image:
docker run --entrypoint /bin/bash --rm -it -v /path/to/data:/data:ro -v /path/to/output:/out nipreps/nirodents:latest
and then at the bash prompt:
artsBrainExtraction /data/sub-01_T2w.nii.gz -o /out/
Let me know if you need any more help.
All the best,