resseg-ijcars

(★ 19)

Code, data and model for Pérez-García et al. 2021, "A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections"

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Tutorial about combining PyTorch and NiftyNet for deep learning and medical image computing

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resector ★ 14

Algorithm to simulate resection surgery on brain MRI scans. Published in MICCAI 2020, extended in IJCARS.

Python

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  • .gitignore
  • constants.py
  • datasets.py
  • engine.py
  • estimate_aleatoric_uncertainty.py
  • estimate_epistemic_uncertainty.py
  • evaluate.py
  • infer.py
  • LICENSE
  • loss.py
  • main.py
  • models.py
  • observers.py
  • README.md
  • register_all.zsh
  • requirements.txt
  • run_robex.zsh
  • utils.py
  • visualization.py

# Use via CDN

jsDelivr

jsDelivr serves any public GitHub repository as a CDN with zero setup. Pick a version and a file to get a ready-to-paste link and snippet.

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Command Glossary

Commands referenced in this DOCs, explained below.

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conda create

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Create new conda environments.

conda create {{[-y|--yes]}} {{[-n|--name]}} py39 python=3.9 "numpy>=1.11" scipy

Create a new environment named `py39`, install Python 3.9, NumPy v1.11 or above in it, and the latest stable version of SciPy. Say yes to all confirmations:

conda create {{[-n|--name]}} myenv --file {{file1.yml}} --file {{file2.yml}}

Create a new environment named `myenv` and install packages listed in files:

conda create {{[-p|--prefix]}} {{path/to/myenv}}

Create a new environment at a custom path (i.e. prefix):

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conda install

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Install packages into an existing conda environment.

conda install {{package1 package2 ...}}

Install one or more package into the currently active conda environment:

conda install {{[-c|--channel]}} conda-forge {{package}}

Install a single package into the currently active conda environment using channel conda-forge:

conda install {{[-c|--channel]}} conda-forge --override-channels {{package}}

Install a single package into the currently active conda environment using channel conda-forge and ignoring other channels:

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pip install

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Install Python packages.

pip install {{package1 package2 ...}}

Install one or more packages:

pip install {{package1 package2 ...}} {{[-U|--upgrade]}}

Upgrade all specified packages to the latest version, installing any that are not already present:

pip install {{package}}=={{version}}

Install a specific version of a package:

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python

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Python language interpreter.

python

Start a REPL (interactive shell):

python {{path/to/file.py}}

Execute a specific Python file:

python -i {{path/to/file.py}}

Execute a specific Python file and start a REPL:

// repository documentation