Conversation
github-project-automation
Bot
moved this to Submitted Implementations
in MHub Submissions
- config used for whole NLST processing (deepcac_dicom_simple.yml)
- update model dirctory aim_deepcac2 -> deepcac2 - update entrypoint cmd to use default workflow
- ensure file name is correct (without trailing url query string ?..) - use env variables for better readability
nnunet 1.7.x depends on dicom2nifti, and newer dicom2nifti pulled in pydicom 3.x, which breaks mhubio, thedicomsort, and wsidicom (all require pydicom <3). At the same time, scipy allowed numpy 2.x, but pydicom-seg and wsidicom require numpy <2, and compiled libraries (e.g., SimpleITK, scipy) were built against NumPy 1.x, causing runtime errors. The environment became inconsistent because dependencies were not pinned and later installs overrode earlier constraints. Fix by pinning: dicom2nifti<2.6, pydicom==2.4.4, numpy==1.26.4. ISSUE: nnunet 1.7.x → dicom2nifti dicom2nifti 2.6.x → pydicom>=3.0.0 nnunet 1.7.x → numpy FIX: dicom2nifti<2.6 - avoids pydicom>=3 pydicom==2.4.4 - satisfies mhubio and stays <3 for thedicomsort/wsidicom numpy==1.26.4 - satisfies scipy while staying <2 for pydicom-seg/wsidicom
- test case used: NLST, 100002, T0 (1.2.840.113654.2.55.257926562693607663865369179341285235858) - test files were generated following the documentation () - test files are published via Zenodo under https://doi.org/10.5281/zenodo.19921180 and can be downloaded under https://zenodo.org/records/19921180
- parses the input directory for files matching `(\d+).nii.gz`
- the file-name is kept inside the MHub.ai run engine under the key `pid`
- and included in the report as `{"PatientID": "file-name"}`
- upload new version under https://doi.org/10.5281/zenodo.19921552
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Test Procedure