Including MouseIn template in fmriprep-rodents

Summary of what happened:

I am trying to use one of the other templates than the standard (fischer344). I have aquired the MouseIn template using the Python API, and I can indeed find the tpl-MouseIn template in expected path (.cache/templateflow/), but when I run fmriprep-rodents, it is not able to find the template.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run --cleanenv fmriprep-rodents-latest.simg ~/Desktop/thesis/data/rsfMRI_example_bids_reoriented/ ~/Desktop/thesis/data/output_dir/ participant --skip-bids-validation --skull-strip-t1w force --output-spaces MouseIn


latest fmriprep-rodents image

Environment (Docker, Singularity, custom installation):


Data formatted according to a validatable standard? Please provide the output of the validator:

passes bids tests

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

Hi @KFDK -

As I wrote in our other discussion, fMRIPrep-Rodents is still in its very early stages and is not yet working with any templates other than fisher344. It’s on our list of things to do, but it might take a while to get around to. If you’d like to help us get it up and running sooner, the maintainers would gratefully accept your contribution as a pull request to our github.