Metadata-Version: 2.1
Name: mrsegmentator
Version: 1.0.1
Summary: Robust Multi-Modality Segmentation of 40 Classes in MRI and CT Sequences
Home-page: https://github.com/hhaentze/mrsegmentator
Author: Hartmut Häntze
Author-email: hartmut.haentze@charite.de
Project-URL: Bug Tracker, https://github.com/hhaentze/mrsegmentator/issues
Project-URL: repository, https://github.com/hhaentze/mrsegmentator
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: POSIX :: Linux
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.11
Description-Content-Type: text/markdown
Requires-Dist: nnunetv2==2.2.1
Requires-Dist: argparse

<h2 align="center"> MRSegmentator: Robust Multi-Modality Segmentation of 40 Classes in MRI and CT Sequences </h2>

***

<div align="center">
<a href="https://github.com/hhaentze/MRSegmentator/actions"><img alt="Continuous Integration" src="https://github.com/hhaentze/MRSegmentator/actions/workflows/ci.yml/badge.svg"></a>
<a href="https://github.com/hhaentze/MRSegmentator/blob/master/License.txt"><img alt="License: Apache" src="https://img.shields.io/badge/License-Apache_2.0-blue.svg"></a>  
<a href="https://test.pypi.org/project/mrsegmentator"><img alt="PyPI" src="https://img.shields.io/pypi/v/mrsegmentator"></a>  
<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
</div>

> Detect and segment 40 classes in MRI scans of the abdominal / pelvic / thorax region


Contrary to CT scans, where tools for automatic multi-structure segmentation are quite mature, segmentation tasks in MRI scans are often either focused on the brain region or on a subset of few organs in other body regions. MRSegmentator aims to extend this and accurately segment 40 organs and structures in human MRI scans of the abdominal, pelvic and thorax regions. The segmentation works well on different sequence types, including T1- and T2-weighted, Dixon sequences and even CT images.

![Sample Image](images/MRSegmentator.png)

## Installation
1. Install [PyTorch](https://pytorch.org/get-started/locally/) based on your system requirements
2. Install MRSegmentator with pip 
3. Download the weights and extract them into your model directory

Example workflow:
```bash
# Create virtual environment
conda create -n mrseg python=3.11 pip
conda activate mrseg

# Install pytorch
conda  install pytorch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 pytorch-cuda=11.7 -c pytorch -c nvidia

# Install MRSegmentator
python -m pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple mrsegmentator

# Inference
mrsegmentator  \
--modeldir "/sc-projects/sc-proj-cc06-ag-ki-radiologie/Niere/ukbb/ckpts/mr_segmentator_weights/" \
--input <nifti file or directory> \
--outdir <directory> 

# Download Weights (TODO) (Currently the weights are stored on the cluster)
# wget https://www.url-placeholder.de/weights.zip
# unzip weights.zip
```

## Inference
MRSegmentator segments all .nii and .nii.gz files in an input directory and writes segmentations to the specified output directory. MRSegmentator was trained on images in LPS orientation and automatically transforms input images accordingly. Afterwards, the segmenation's orientation will be changed back to match the original image. If you are certain that your images are in the LPS orientation you can skip this preoprocessing step by setting the ```--is_LPS``` flag (this significantly reduces runtime). MRSegmentator requires a lot of memory and can run into OutOfMemory exceptions when used on very large images (e.g. some CT scans). You can reduce memory usage by setting ```--split_level``` to 1 or 2. Be aware that this increases runtime and possibly reduces segmentation performance.

```bash
mrsegmentator --modeldir <model directory> \
    --input <input directory or file> \
    --outdir <output directory> 
```

Options:
```bash
--modeldir <str> [required]  # model directory
--input <str> [required] # input directory or file
--outdir <str> [required] # output directory

--fold <int> # use only a single model for inference 
--crossval # Run all 5 models individually. Useful to analyse differences between the models.

--is_LPS # if your images are in LPS orientation you can set this flag to skip one preprocessing step. This decreases runtime
--postfix <str> # postfix that will be added to segmentations. Default: "seg"
--cpu_only # don't use a gpu
--verbose
--batchsize <int> # how many images can be loaded to memory at the same time, ideally this should equal the dataset size
--nproc <int> # number of processes
--nproc_export <int> # number of processes for exporting the segmentations
--split_level <int> # split images to reduce memory usage. Images are split recusively: A split level of x will produce 2^x smaller images.
```

## Python API
```python
from mrsegmentator import inference
import os

modeldir = "mrseg_weights"
outdir = "outputdir"
images = [f.path for f in os.scandir("image_dir")]
folds = [0]

inference.infer(modeldir, outdir, images, folds)

```


## Class details

|Index|Class|
| :-------- | :------- |
| 0 | background |
| 1 | spleen |
| 2 | right_kidney |
| 3 | left_kidney |
| 4 | gallbladder |
| 5 | liver |
| 6 | stomach |
| 7 | pancreas |
| 8 | right_adrenal_gland |
| 9 | left_adrenal_gland |
| 10 | left_lung |
| 11 | right_lung |
| 12 | heart |
| 13 | aorta |
| 14 | inferior_vena_cava |
| 15 | portal_vein_and_splenic_vein |
| 16 | left_iliac_artery |
| 17 | right_iliac_artery |
| 18 | left_iliac_vena |
| 19 | right_iliac_vena |
| 20 | esophagus |
| 21 | small_bowel |
| 22 | duodenum |
| 23 | colon |
| 24 | urinary_bladder |
| 25 | spine |
| 26 | sacrum |
| 27 | left_hip |
| 28 | right_hip |
| 29 | left_femur |
| 30 | right_femur |
| 31 | left_autochthonous_muscle |
| 32 | right_autochthonous_muscle |
| 33 | left_iliopsoas_muscle |
| 34 | right_iliopsoas_muscle |
| 35 | left_gluteus_maximus |
| 36 | right_gluteus_maximus |
| 37 | left_gluteus_medius |
| 38 | right_gluteus_medius |
| 39 | left_gluteus_minimus |
| 40 | right_gluteus_minimus |
