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312 Open 2,554 Closed
312 Open 2,554 Closed
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Issues list

Indicate deepseg model enhancement category: improves performance/results of an existing feature sct_deepseg context: Global entry point for all deep learning segmentation methods
#4518 opened Jun 6, 2024 by jcohenadad 6.4
1
@joshuacwnewton
1
FileNotFoundError: when using type=im with algo=centermassrot bug category: fixes an error in the code sct_register_multimodal context:
#4516 opened Jun 6, 2024 by jcohenadad
6
macOS runners take an inconsistent amount of time to run, sporadically triggering the -h profiling test CI category: TravisCI, GitHub Actions, etc. OS: macOS
#4515 opened Jun 6, 2024 by joshuacwnewton
Provide better instructions when Windows username contains spaces bug category: fixes an error in the code OS: Windows (native)
#4513 opened Jun 5, 2024 by joshuacwnewton
3
Mask creation is no more required for cropping documentation category: readthedocs, sourceforge, or SCT courses
#4512 opened Jun 5, 2024 by jcohenadad
Output softseg from MONAI inference is not in the range [0, 1] bug category: fixes an error in the code sct_deepseg context: Global entry point for all deep learning segmentation methods
#4507 opened Jun 3, 2024 by joshuacwnewton 6.4
1
@joshuacwnewton
4
Thresholding during image registration bug category: fixes an error in the code sct_register_multimodal context:
#4504 opened May 31, 2024 by plbenveniste 6.4
@joshuacwnewton
The threshold parameter of sct_deepseg doesn't work with the model seg_sc_contrast_agnostic for soft segmentation. bug category: fixes an error in the code sct_deepseg context: Global entry point for all deep learning segmentation methods
#4503 opened May 31, 2024 by simonqueric 6.4
1
@joshuacwnewton
8
Develop new method to register odd and even chunks on 3D volumes feature category: new functionality good internship project SCT API: registration context:
#4502 opened May 31, 2024 by jcohenadad
3
sct_run_batch does not seem robust to BIDS format bug category: fixes an error in the code sct_run_batch context:
#4500 opened May 30, 2024 by maxradx
3
Dipy denoising functions are duplicated between sct_maths and sct_denoising_onlm/sct_dmri_denoise_patch2self refactoring category: improves code structure without affecting user-facing functionality
#4492 opened May 24, 2024 by joshuacwnewton
Add postprocessing functionality for the new monai/nnunet models feature category: new functionality sct_deepseg context: Global entry point for all deep learning segmentation methods
#4481 opened May 14, 2024 by naga-karthik 6.4
1
@naga-karthik
Straightening is not a bijective transformation bug category: fixes an error in the code sct_straighten_spinalcord context:
#4477 opened May 14, 2024 by jcohenadad 6.4
1
@mguaypaq
25
Project discs orthogonally to the spinal cord segmentation or centerline feature category: new functionality sct_label_utils context: sct_label_vertebrae context:
#4476 opened May 13, 2024 by jcohenadad
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
@joshuacwnewton
1
Refactor sct_deepseg to store model orientation in model dict refactoring category: improves code structure without affecting user-facing functionality sct_deepseg context: Global entry point for all deep learning segmentation methods
#4450 opened Apr 22, 2024 by joshuacwnewton
4
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
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
1
@joshuacwnewton
1
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
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