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309 Open 2,533 Closed
309 Open 2,533 Closed
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Issues list

Custom argparse formatter fails for blank lines in multiline strings bug category: fixes an error in the code SCT API: utils.py context:
#4471 opened May 6, 2024 by joshuacwnewton
@joshuacwnewton
1
Indicate versions of sct_deepseg models
#4465 opened May 1, 2024 by jcohenadad 6.4
1
@joshuacwnewton
5
Should we issue certificates for the SCT course? documentation category: readthedocs, sourceforge, or SCT courses priority:LOW user requested Raised by user on the SCT forum/email/GitHub. Be sure to notify them when fixed in a release.
#4464 opened Apr 30, 2024 by joshuacwnewton
Fix issues with sct_deepseg rootlets QC report bug category: fixes an error in the code sct_deepseg context: Global entry point for all deep learning segmentation methods sct_qc context:
#4461 opened Apr 25, 2024 by joshuacwnewton 6.4
1
Customize image disposition QC with sct_deepseg_lesion feature category: new functionality
#4458 opened Apr 24, 2024 by NathanMolinier 6.4
@joshuacwnewton
1
Refactor sct_deepseg to store model orientation in model dict
#4450 opened Apr 22, 2024 by joshuacwnewton
4
-c (contrast) field is not useful or 95% of deepseg models (and is unintuitive for contributors) bug category: fixes an error in the code sct_deepseg context: Global entry point for all deep learning segmentation methods
#4445 opened Apr 18, 2024 by joshuacwnewton
2
Change -install-task to -install feature category: new functionality sct_deepseg context: Global entry point for all deep learning segmentation methods
#4435 opened Apr 13, 2024 by jcohenadad 6.4
@joshuacwnewton
1
SCT uses the reverse convention for orientation strings compared to nibabel/BIDS/FSL: 'RPI' (-) vs. 'LAS' (+)
#4419 opened Apr 3, 2024 by NathanMolinier
6
Image objects have mixed, inconsistent usage of self.affine and self.header refactoring category: improves code structure without affecting user-facing functionality
#4415 opened Mar 25, 2024 by joshuacwnewton
1
Upload batch_processing.sh CSV files as artifacts during CI run CI category: TravisCI, GitHub Actions, etc. good first issue Issues that new contributors can easily work on script: batch_processing.sh context: tests context: unit, integration, or functional tests
#4412 opened Mar 22, 2024 by joshuacwnewton
Warning with numpy.longdouble gets thrown on WSL when calling SCT functions bug category: fixes an error in the code OS: Windows (WSL) priority:LOW upstream Issue caused by software dependencies
#4411 opened Mar 20, 2024 by sandrinebedard
@joshuacwnewton
8
File permission error during SCT installation installation category: install_sct or pip/setup.py OS: Windows (WSL) SCT API: download.py context:
#4410 opened Mar 20, 2024 by mguaypaq 6.4
Investigate RuntimeWarnings raised by test suite during numerical calculations maintenance tests context: unit, integration, or functional tests
#4407 opened Mar 18, 2024 by joshuacwnewton
Update pandas to >=2.0.0 to resolve DeprecationWarnings from up-to-date numpy package maintenance upstream Issue caused by software dependencies
#4406 opened Mar 18, 2024 by joshuacwnewton
Test initial_disc_too_low doesn't work as intended, triggering a numpy DeprecationWarning bug category: fixes an error in the code tests context: unit, integration, or functional tests
#4405 opened Mar 18, 2024 by joshuacwnewton
Address new MONAI/nnUNet-related warnings raised in test suite
#4404 opened Mar 18, 2024 by joshuacwnewton
Add developer git hooks to .githooks/ folder to make dev environment setup easier git/github category: meta-discussion about project management and development practices
#4399 opened Mar 11, 2024 by joshuacwnewton
Usage of the sct_analyze_lesion -f option is unclear (percentage distributions) documentation category: readthedocs, sourceforge, or SCT courses sct_analyze_lesion context:
#4394 opened Mar 7, 2024 by jqmcginnis 6.4
@joshuacwnewton
5
Update the SCT changelog to clearly indicate upstream changes to the PAM50 template (e.g. Frostell et al. levels)
#4388 opened Mar 1, 2024 by jcohenadad
5
Displacement of a sub-panel in QC report bug category: fixes an error in the code sct_qc context:
#4386 opened Feb 29, 2024 by jcohenadad
Replace SCT's custom build workflow for ANTs with officially-distributed, prebuilt ANTs binaries CI category: TravisCI, GitHub Actions, etc. maintenance
#4376 opened Feb 15, 2024 by kousu
1
Use anonymous hyperlinks (' <>'__) by default over named hyperlinks (' <>'_) in Sphinx documentation documentation category: readthedocs, sourceforge, or SCT courses
#4371 opened Feb 14, 2024 by joshuacwnewton
Slow imports maintenance
#4370 opened Feb 14, 2024 by joshuacwnewton
6
Allow QC report to display segmentations with sagittal view without SC segmentation feature category: new functionality
#4365 opened Feb 8, 2024 by NathanMolinier
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