Cannot find example data such as "data_test_macaque_processed.zip"

[Cdefgpku]

Hi, I am trying to run the example "Plot the results of a segmentation with SPM-based pipeline T1xT2", but there is an error in the line "data_path = load_test_data("data_test_macaque_processed")". It says : AssertionError: Error, data_zip = C:\Users\dell\data_macapype\data_test_macaque_processed.zip not found . I checked the C:\Users\dell\data_macapype folder and fount it empty. I also try to run other examples and met the similar error when trying to load the example data.

I would hope to ask where to find or to download the example data. Thank you very much!

[davidmeunier79]

Hello, sry just noticed your message. Indeed the documentation is not very well done, sorry about that . Howver, the part you are mentionning is when the preprocessing is already done. If you want to test processing of macapype on real data, I would advice to look at the github actions with testing on the docker part:

https://github.com/Macatools/macapype/blob/838be2720f2077a5522ebfc7a700398172a5cc0b/.github/workflows/build_on_prerelease.yml#L76C13-L76C50

And in particular the commands:

docker pull macatools/macapype:latest
wget --no-check-certificate --content-disposition  "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI

And finally: docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 where the path "/home/runner/work/macapype/macapype/" will depend on where you downloaded the dataset.

If you have installed macapype as a package, and all the underlying softwares, you can run: segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2