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SIMEXP / giga_auto_qc

Automatic quality control for fMRIPrep outputs aimed for large dataset
MIT License
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Fix/anat fast track derivative #35

Open htwangtw opened 7 months ago

htwangtw commented 7 months ago

Closes #32 Closes #33 Closes #34

Solution: ignore anatomical metrics if anat/ is not present

codecov-commenter commented 7 months ago

Codecov Report

Attention: Patch coverage is 0% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 10.85%. Comparing base (c7b951f) to head (adf5437).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35/graphs/tree.svg?width=650&height=150&src=pr&token=TYE4UURNTQ&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP)](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP) ```diff @@ Coverage Diff @@ ## main #35 +/- ## =========================================== - Coverage 94.46% 10.85% -83.62% =========================================== Files 5 8 +3 Lines 235 350 +115 =========================================== - Hits 222 38 -184 - Misses 13 312 +299 ``` | [Files](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP) | Coverage Δ | | |---|---|---| | [giga\_auto\_qc/workflow.py](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35?src=pr&el=tree&filepath=giga_auto_qc%2Fworkflow.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP#diff-Z2lnYV9hdXRvX3FjL3dvcmtmbG93LnB5) | `8.10% <0.00%> (-77.61%)` | :arrow_down: | | [giga\_auto\_qc/tests/test\_assessments.py](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35?src=pr&el=tree&filepath=giga_auto_qc%2Ftests%2Ftest_assessments.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP#diff-Z2lnYV9hdXRvX3FjL3Rlc3RzL3Rlc3RfYXNzZXNzbWVudHMucHk=) | `7.27% <0.00%> (ø)` | | | [giga\_auto\_qc/assessments.py](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35?src=pr&el=tree&filepath=giga_auto_qc%2Fassessments.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP#diff-Z2lnYV9hdXRvX3FjL2Fzc2Vzc21lbnRzLnB5) | `5.33% <0.00%> (-90.45%)` | :arrow_down: | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/SIMEXP/giga_auto_qc/pull/35/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=SIMEXP)
htwangtw commented 6 months ago

@clarkenj On compute canada you can pull the build of this PR to test it out apptainer build giga_auto_qc_unstable.simg docker://haotingwang/giga_auto_qc:unstable

htwangtw commented 6 months ago

Request from @clarkenj to be addressed: when supplying anatomical only directory, calculate the anatomical dice Not addressing this as it turned out to be more complicated than I thought.