Closed LeSasse closed 4 months ago
When I remove
masks:
- inherit
from the marker it works.
I did not actually define a mask in the preprocessor.
I have re-opened it, because the AOMIC ID1000 datagrabber does have BOLD_masks that I should be able to inherit in the marker extraction. But I think the preprocessor for Smoothing from #161 is messing with it.
@LeSasse I believe I've found the bug and it's that when we warp parcellation via ANTs, it somehow adds an extra axis when loading via nibabel. If you try with a parcellation without the need to warp, it'll be ok. So, I've added an explicit np.squeeze
in nilearn's math_img
. Check this branch out for your run and let me know if it solves it and you get correct results.
PR Preview Action v1.4.7 :---: Preview removed because the pull request was closed. 2024-04-10 17:09 UTC
Works like a charm!
All modified and coverable lines are covered by tests :white_check_mark:
Project coverage is 100.00%. Comparing base (
0fde637
) to head (c0c893b
).
Is there an existing issue for this?
Current Behavior
When I apply a mask in FC extraction using a YAML pipeline it fails.
Expected Behavior
I would like it to apply the mask correctly and not fail.
Steps To Reproduce
datagrabber: kind: DataladAOMICID1000
preprocess: kind: Smoothing using: "nilearn" "on": "BOLD" smoothing_params: fwhm: 10
storage: kind: HDF5FeatureStorage uri: data/aomic_id1000.hdf5
markers:
queue: jobname: smoothing_test kind: HTCondor collect: on_success_only env: kind: venv name: env mem: 20G verbose: 8 pre_run: | source /data/group/appliedml/tools/ants_2.5.0/ants.sh
Relevant log output