Working on preprocessing docker
Browse files- README.md +9 -118
- docker/preprocess.Dockerfile +34 -0
- poetry.lock +280 -263
- pyproject.toml +1 -1
- scripts/preprocess.py +0 -20
- scripts/preprocess.sh +103 -0
README.md
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conda create --name pyment python=3.9
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```
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### Via pip
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Although the package is not currently available on PyPI, it is possible to install it via pip directly from git, using the following command:
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```
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pip install git+https://github.com/estenhl/pyment-public
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```
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### Manually
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It is also possible to download the package from git and manually install it (the following demonstrates how its done on a Unix-based OS).
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```
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git clone git@github.com:estenhl/pyment-public.git
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cd pyment-public
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pip install -r requirements.txt
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pip install -e .
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```
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### Verification
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There are two ways the installation can be verified. By running the unit-tests (while still in the pyment-public folder):
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```
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pytest tests
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```
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If this fails, it is probably the prerequisites that has not been installed properly, rerun
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the ```pip install -r requirements.txt```-command and monitor the output. You can also check that the package is properly installed on the system (not from the pyment-public folder):
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```
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python -c "import pyment"
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```
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If this fails, it is the ```pip install -e .```-command that failed, return to that and check for error messages.
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## Publications
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This is an overview of the publications from where the pretrained models originate. The shorthand-column denotes the name that is used to refer to the publications below. Note that the corresponding author is not necessarily equivalent to what is listed in the publication, but instead refers to the author in charge of the modelling.
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| Title | Abbreviation | Publication year | Corresponding author | Citation |
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| --- | :-: | :-: | :-: | :-: |
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| [Deep neural networks learn general and clinically relevant representations of the ageing brain](https://doi.org/10.1016/j.neuroimage.2022.119210) | brain-age-general | 2022 | [Esten Høyland Leonardsen](mailto:estenhl@uio.no) | [.bib](citations/brain-age-general.bib) |
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| [Genetic architecture of brain age and its causal relations with brain and mental disorders](https://doi.org/10.1038/s41380-023-02087-y) | brain-age-genetics | 2023 | [Esten Høyland Leonardsen](mailto:estenhl@uio.no) | [.bib](citations/brain-age-genetics.bib) |
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| [Constructing personalized characterizations of structural brain aberrations in patients with dementia and mild cognitive impairment using explainable artificial intelligence](https://doi.org/10.1101/2023.06.22.23291592) | explainable-dementia | 2024 | [Esten Høyland Leonardsen](mailto:estenhl@uio.no) | [.bib](citations/explainable-dementia.bib) |
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## Architectures
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This is an overview of the model architectures used in the pretrained models.
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| Name | Abbreviation | Description |
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| --- | :-: | --- |
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| RegressionSFCN | sfcn-reg | Base SFCN with a regression prediction head |
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| RankingSFCN | sfcn-rank | Base SFCN with a ranking prediction head for regression problems |
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| SoftClassificationSFCN | sfcn-sm | Base SFCN with a softmax prediction head, as per the original SFCN |
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| BinarySFCN | sfcn-bin | Base SFCN with a binary prediction head for binary classification problems |
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## Models
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This is an overview of the actual pretrained models. The names are what should be used in the python-code to load the correct weights. Note that the names are not necessarily unique, but the tuple (name, architecture) is. The training set size refers to _samples_, not _participants_, and can thus have multiple session per participant.
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| Name | Architecture | Source publication | Description | Training sample size | Expected out-of-sample error | URL |
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| :-: | :-: | :-: | --- | :-: | :-: | :-: |
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| brain-age-2022 | sfcn-reg | [brain-age-general](http://doi.org/10.1016/j.neuroimage.2022.119210) | Brain age regression model trained on heterogeneous dataset | 34285 | MAE=3.9 | [link](https://api.github.com/repos/estenhl/pyment-public/git/blobs/f87a66558433308bb8a5ecfb6aaa784811c5cd45) |
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| brain-age-2022 | sfcn-rank | [brain-age-general](http://doi.org/10.1016/j.neuroimage.2022.119210) | Brain age ranking model trained on heterogeneous dataset | 34285 | MAE=5.92 | [link](https://api.github.com/repos/estenhl/pyment-public/git/blobs/5d1bc5fc66327eb905acf81d9956f0391277b078) |
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| brain-age-2022 | sfcn-sm | [brain-age-general](http://doi.org/10.1016/j.neuroimage.2022.119210) | Brain age soft classification model trained on heterogeneous dataset | 34285 | MAE=5.04 | [link](https://api.github.com/repos/estenhl/pyment-public/git/blobs/7b4f7bf4c989b80877b0bc0efe8b5125157788b5) |
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| dementia-2024-fold-X | sfcn-bin | [explainable-dementia](http://doi.org/10.1101/2023.06.22.23291592) | Dementia classification model trained on multiple datasets.<br />Contains mostly patients with probable AD, but also other aetiologies<br />Fold number refers to the fold that were held out during training, if no fold is specified the first is used. | 1366 | | [fold 0](https://api.github.com/repos/estenhl/pyment-public/git/blobs/1f43aafd2461d7e5b4f9ebb6d62e0f2ab363e1b8)<br /> [fold 1](https://api.github.com/repos/estenhl/pyment-public/git/blobs/a0da6b724f3c1477ae2f461c49a91b7d2f46ac72)<br /> [fold 2](https://api.github.com/repos/estenhl/pyment-public/git/blobs/cec0eb79f043a3415f5ab13977dfda24e1f7dc30)<br /> [fold 3](https://api.github.com/repos/estenhl/pyment-public/git/blobs/c885fee44d4839d37d8bcdfd970391788ee85004)<br /> [fold 4](https://api.github.com/repos/estenhl/pyment-public/git/blobs/35d3b0343b83a9851a140cab7baed2dd36e35185)<br /> |
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## License
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The code and models in this repo is released under the [CC-BY-NC license](LICENSE.md) for <b>non-commercial</b> use.
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## Citations
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If you use a pretrained from this model, please cite the originating publication:
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### brain-age-general
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```
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@article{leonardsen2022deep,
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title = {Deep neural networks learn general and clinically relevant representations of the ageing brain},
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author = {Esten H. Leonardsen and Han Peng and Tobias Kaufmann and Ingrid Agartz and Ole A. Andreassen and Elisabeth Gulowsen Celius and Thomas Espeseth and Hanne F. Harbo and Einar A. Høgestøl and Ann-Marie de Lange and Andre F. Marquand and Didac Vidal-Piñeiro and James M. Roe and Geir Selbæk and Øystein Sørensen and Stephen M. Smith and Lars T. Westlye and Thomas Wolfers and Yunpeng Wang},
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journal = {NeuroImage},
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volume = {256},
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pages = {119210},
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year = {2022},
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issn = {1053-8119},
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doi = {https://doi.org/10.1016/j.neuroimage.2022.119210},
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url = {https://www.sciencedirect.com/science/article/pii/S1053811922003342},
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}
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```
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### explainable-dementia
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```
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@article {leonardsen2024constructing,
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title={Constructing personalized characterizations of structural brain aberrations in patients with dementia and mild cognitive impairment using explainable artificial intelligence},
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author={Esten H. Leonardsen and Karin Persson and Edvard Gr{\o}dem and Nicola Dinsdale and Till Schellhorn and James M. Roe and Didac Vidal-Pi{\~n}eiro and {\O}ystein S{\o}rensen and Tobias Kaufmann and Eric Westman and Andre Marquand and Geir Selb{\ae}k and Ole A. Andreassen and Thomas Wolfers and Lars T. Westlye and Yunpeng Wang and Alzheimer{\textquoteright}s Disease Neuroimaging Initiative and Australian Imaging Biomarkers and Lifestyle flagship study of ageing},
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journal={medRxiv},
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year={2024},
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publisher={Cold Spring Harbor Laboratory Press},
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doi={https://doi.org/10.1101/2023.06.22.23291592},
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url={https://www.medrxiv.org/content/early/2024/02/22/2023.06.22.23291592},
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}
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```
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### brain-age-genetics
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```
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@article{leonardsen2023genetic,
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title={Genetic architecture of brain age and its causal relations with brain and mental disorders},
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author={Leonardsen, Esten H and Vidal-Pi{\~n}eiro, Didac and Roe, James M and Frei, Oleksandr and Shadrin, Alexey A and Iakunchykova, Olena and de Lange, Ann-Marie G and Kaufmann, Tobias and Taschler, Bernd and Smith, Stephen M and others},
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journal={Molecular Psychiatry},
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volume={28},
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number={7},
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pages={3111--3120},
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year={2023},
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publisher={Nature Publishing Group UK London},
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issn = {1476-5578},
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doi = {https://doi.org/10.1038/s41380-023-02087-y},
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url = {https://www.nature.com/articles/s41380-023-02087-y},
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}
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```
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## Build docker container for preprocessing
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docker build \
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-f docker/preprocess.Dockerfile \
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-t pyment/preprocessing:1.0.0 \
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--build-arg CHECKPOINTS_FOLDER=<path_to_fastsurfer_checkpoints>
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.
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## Run docker container for preprocessing
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docker run --rm -v <path_to_input>:/input -v <path_to_ouput>:/output -v <path_to_licenses>:/licenses --gpus all pyment/preprocessing:1.0.0
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docker/preprocess.Dockerfile
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FROM python:3.10.2-slim
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#ARG CHECKPOINTS_FOLDER
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RUN apt-get update && apt-get install -y \
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apt-utils git \
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&& rm -rf /var/lib/apt/lists/*
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RUN mkdir -p /envs && python -m venv /envs/fastsurfer
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RUN mkdir /repos && \
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git clone https://github.com/Deep-MI/FastSurfer.git /repos/FastSurfer \
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&& cd /repos/FastSurfer \
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&& git checkout v2.0.1
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ENV FASTSURFER_HOME=/repos/FastSurfer
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# Install requirements. The SimpleITK version in requirements.txt is yanked,
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# so we need to install it manually and remove it from requirements.txt.
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RUN /envs/fastsurfer/bin/pip install --upgrade pip && \
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/envs/fastsurfer/bin/pip install simpleitk==2.1.1.2 --upgrade && \
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sed -i '/simpleitk/d' ${FASTSURFER_HOME}/requirements.txt && \
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/envs/fastsurfer/bin/pip install -r ${FASTSURFER_HOME}/requirements.txt
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#COPY ${CHECKPOINTS_FOLDER} ${FASTSURFER_HOME}/FastSurferCNN/checkpoints
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COPY checkpoints ${FASTSURFER_HOME}/FastSurferCNN/checkpoints
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RUN mkdir /scripts
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COPY scripts/preprocess.sh /scripts/preprocess.sh
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CMD ["/bin/sh", "/scripts/preprocess.sh", \
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"--license", "/licenses/freesurfer.txt", \
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"--python", "/envs/fastsurfer/bin/python", \
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"/input", "/output"]
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poetry.lock
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[[package]]
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name = "absl-py"
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version = "2.3.
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description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
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optional = false
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python-versions = ">=3.8"
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groups = ["main"]
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files = [
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{file = "absl_py-2.3.
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]
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[[package]]
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[[package]]
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name = "fastsurfer"
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version = "2.
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description = "A fast and accurate deep-learning based neuroimaging pipeline"
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optional = false
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python-versions = ">=3.10"
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style = ["bibclean", "codespell", "pydocstyle[toml]", "ruff"]
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[package.source]
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type = "
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url = "
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reference = "v2.4.2"
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resolved_reference = "7e5334356e5abc0b600c11d6e9890e386d176433"
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[[package]]
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name = "filelock"
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[[package]]
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name = "fonttools"
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version = "4.58.
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description = "Tools to manipulate font files"
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optional = false
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python-versions = ">=3.9"
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groups = ["main"]
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files = [
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[package.extras]
|
|
@@ -445,67 +443,67 @@ tqdm = ["tqdm"]
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|
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[[package]]
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name = "grpcio"
|
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-
version = "1.73.
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description = "HTTP/2-based RPC framework"
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]
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[package.extras]
|
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protobuf = ["grpcio-tools (>=1.73.
|
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name = "h5py"
|
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@@ -780,14 +778,14 @@ test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]
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|
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|
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description = "Python implementation of John Gruber's Markdown."
|
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[package.extras]
|
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name = "narwhals"
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|
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description = "Extremely lightweight compatibility layer between dataframe libraries"
|
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[package.extras]
|
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@@ -996,8 +994,8 @@ dask = ["dask[dataframe] (>=2024.8)"]
|
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duckdb = ["duckdb (>=1.0)"]
|
| 997 |
ibis = ["ibis-framework (>=6.0.0)", "packaging", "pyarrow-hotfix", "rich"]
|
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modin = ["modin"]
|
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|
| 1000 |
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polars = ["polars (>=0.20.
|
| 1001 |
pyarrow = ["pyarrow (>=11.0.0)"]
|
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pyspark = ["pyspark (>=3.5.0)"]
|
| 1003 |
pyspark-connect = ["pyspark[connect] (>=3.5.0)"]
|
|
@@ -1420,114 +1418,139 @@ xml = ["lxml (>=4.9.2)"]
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| 1420 |
|
| 1421 |
[[package]]
|
| 1422 |
name = "pillow"
|
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version = "11.
|
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description = "Python Imaging Library (Fork)"
|
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|
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[package.extras]
|
| 1513 |
-
docs = ["furo", "olefile", "sphinx (>=8.2)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
|
| 1514 |
fpx = ["olefile"]
|
| 1515 |
mic = ["olefile"]
|
| 1516 |
test-arrow = ["pyarrow"]
|
| 1517 |
-
tests = ["check-manifest", "coverage (>=7.4.2)", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout", "trove-classifiers (>=2024.10.12)"]
|
| 1518 |
typing = ["typing-extensions ; python_version < \"3.10\""]
|
| 1519 |
xmp = ["defusedxml"]
|
| 1520 |
|
| 1521 |
[[package]]
|
| 1522 |
name = "plotly"
|
| 1523 |
-
version = "6.
|
| 1524 |
description = "An open-source interactive data visualization library for Python"
|
| 1525 |
optional = false
|
| 1526 |
python-versions = ">=3.8"
|
| 1527 |
groups = ["main"]
|
| 1528 |
files = [
|
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|
| 1530 |
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|
| 1531 |
]
|
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[package.dependencies]
|
|
@@ -1535,9 +1558,12 @@ narwhals = ">=1.15.1"
|
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| 1535 |
packaging = "*"
|
| 1536 |
|
| 1537 |
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|
| 1538 |
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dev = ["
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| 1539 |
express = ["numpy"]
|
| 1540 |
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kaleido = ["kaleido (=
|
| 1541 |
|
| 1542 |
[[package]]
|
| 1543 |
name = "protobuf"
|
|
@@ -1584,14 +1610,14 @@ test = ["pytest", "pytest-xdist", "setuptools"]
|
|
| 1584 |
|
| 1585 |
[[package]]
|
| 1586 |
name = "pygments"
|
| 1587 |
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version = "2.19.
|
| 1588 |
description = "Pygments is a syntax highlighting package written in Python."
|
| 1589 |
optional = false
|
| 1590 |
python-versions = ">=3.8"
|
| 1591 |
groups = ["main"]
|
| 1592 |
files = [
|
| 1593 |
-
{file = "pygments-2.19.
|
| 1594 |
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{file = "pygments-2.19.
|
| 1595 |
]
|
| 1596 |
|
| 1597 |
[package.extras]
|
|
@@ -1845,67 +1871,58 @@ tests = ["matplotlib (>=3.5.0)", "mypy (>=1.15)", "numpydoc (>=1.2.0)", "pandas
|
|
| 1845 |
|
| 1846 |
[[package]]
|
| 1847 |
name = "scipy"
|
| 1848 |
-
version = "1.
|
| 1849 |
description = "Fundamental algorithms for scientific computing in Python"
|
| 1850 |
optional = false
|
| 1851 |
-
python-versions = ">=3.
|
| 1852 |
groups = ["main"]
|
| 1853 |
files = [
|
| 1854 |
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{file = "scipy-1.
|
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|
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|
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|
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|
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|
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|
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|
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|
| 1886 |
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|
| 1887 |
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|
| 1888 |
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{file = "scipy-1.
|
| 1889 |
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{file = "scipy-1.
|
| 1890 |
-
{file = "scipy-1.
|
| 1891 |
-
{file = "scipy-1.15.3-cp313-cp313t-macosx_12_0_arm64.whl", hash = "sha256:6487aa99c2a3d509a5227d9a5e889ff05830a06b2ce08ec30df6d79db5fcd5c5"},
|
| 1892 |
-
{file = "scipy-1.15.3-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:50f9e62461c95d933d5c5ef4a1f2ebf9a2b4e83b0db374cb3f1de104d935922e"},
|
| 1893 |
-
{file = "scipy-1.15.3-cp313-cp313t-macosx_14_0_x86_64.whl", hash = "sha256:14ed70039d182f411ffc74789a16df3835e05dc469b898233a245cdfd7f162cb"},
|
| 1894 |
-
{file = "scipy-1.15.3-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0a769105537aa07a69468a0eefcd121be52006db61cdd8cac8a0e68980bbb723"},
|
| 1895 |
-
{file = "scipy-1.15.3-cp313-cp313t-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9db984639887e3dffb3928d118145ffe40eff2fa40cb241a306ec57c219ebbbb"},
|
| 1896 |
-
{file = "scipy-1.15.3-cp313-cp313t-musllinux_1_2_aarch64.whl", hash = "sha256:40e54d5c7e7ebf1aa596c374c49fa3135f04648a0caabcb66c52884b943f02b4"},
|
| 1897 |
-
{file = "scipy-1.15.3-cp313-cp313t-musllinux_1_2_x86_64.whl", hash = "sha256:5e721fed53187e71d0ccf382b6bf977644c533e506c4d33c3fb24de89f5c3ed5"},
|
| 1898 |
-
{file = "scipy-1.15.3-cp313-cp313t-win_amd64.whl", hash = "sha256:76ad1fb5f8752eabf0fa02e4cc0336b4e8f021e2d5f061ed37d6d264db35e3ca"},
|
| 1899 |
-
{file = "scipy-1.15.3.tar.gz", hash = "sha256:eae3cf522bc7df64b42cad3925c876e1b0b6c35c1337c93e12c0f366f55b0eaf"},
|
| 1900 |
]
|
| 1901 |
|
| 1902 |
[package.dependencies]
|
| 1903 |
-
numpy = ">=1.
|
| 1904 |
|
| 1905 |
[package.extras]
|
| 1906 |
dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
|
| 1907 |
-
doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.
|
| 1908 |
-
test = ["Cython", "array-api-strict (>=2.
|
| 1909 |
|
| 1910 |
[[package]]
|
| 1911 |
name = "setuptools"
|
|
@@ -2130,14 +2147,14 @@ optree = ["optree (>=0.13.0)"]
|
|
| 2130 |
|
| 2131 |
[[package]]
|
| 2132 |
name = "torchio"
|
| 2133 |
-
version = "0.20.
|
| 2134 |
description = "Tools for medical image processing with PyTorch"
|
| 2135 |
optional = false
|
| 2136 |
python-versions = ">=3.9"
|
| 2137 |
groups = ["main"]
|
| 2138 |
files = [
|
| 2139 |
-
{file = "torchio-0.20.
|
| 2140 |
-
{file = "torchio-0.20.
|
| 2141 |
]
|
| 2142 |
|
| 2143 |
[package.dependencies]
|
|
@@ -2268,14 +2285,14 @@ typing-extensions = ">=3.7.4.3"
|
|
| 2268 |
|
| 2269 |
[[package]]
|
| 2270 |
name = "typing-extensions"
|
| 2271 |
-
version = "4.14.
|
| 2272 |
description = "Backported and Experimental Type Hints for Python 3.9+"
|
| 2273 |
optional = false
|
| 2274 |
python-versions = ">=3.9"
|
| 2275 |
groups = ["main"]
|
| 2276 |
files = [
|
| 2277 |
-
{file = "typing_extensions-4.14.
|
| 2278 |
-
{file = "typing_extensions-4.14.
|
| 2279 |
]
|
| 2280 |
|
| 2281 |
[[package]]
|
|
@@ -2434,4 +2451,4 @@ PyYAML = "*"
|
|
| 2434 |
[metadata]
|
| 2435 |
lock-version = "2.1"
|
| 2436 |
python-versions = ">=3.12"
|
| 2437 |
-
content-hash = "
|
|
|
|
| 2 |
|
| 3 |
[[package]]
|
| 4 |
name = "absl-py"
|
| 5 |
+
version = "2.3.1"
|
| 6 |
description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
|
| 7 |
optional = false
|
| 8 |
python-versions = ">=3.8"
|
| 9 |
groups = ["main"]
|
| 10 |
files = [
|
| 11 |
+
{file = "absl_py-2.3.1-py3-none-any.whl", hash = "sha256:eeecf07f0c2a93ace0772c92e596ace6d3d3996c042b2128459aaae2a76de11d"},
|
| 12 |
+
{file = "absl_py-2.3.1.tar.gz", hash = "sha256:a97820526f7fbfd2ec1bce83f3f25e3a14840dac0d8e02a0b71cd75db3f77fc9"},
|
| 13 |
]
|
| 14 |
|
| 15 |
[[package]]
|
|
|
|
| 279 |
|
| 280 |
[[package]]
|
| 281 |
name = "fastsurfer"
|
| 282 |
+
version = "2.5.0-dev"
|
| 283 |
description = "A fast and accurate deep-learning based neuroimaging pipeline"
|
| 284 |
optional = false
|
| 285 |
python-versions = ">=3.10"
|
|
|
|
| 315 |
style = ["bibclean", "codespell", "pydocstyle[toml]", "ruff"]
|
| 316 |
|
| 317 |
[package.source]
|
| 318 |
+
type = "directory"
|
| 319 |
+
url = "../FastSurfer"
|
|
|
|
|
|
|
| 320 |
|
| 321 |
[[package]]
|
| 322 |
name = "filelock"
|
|
|
|
| 337 |
|
| 338 |
[[package]]
|
| 339 |
name = "fonttools"
|
| 340 |
+
version = "4.58.5"
|
| 341 |
description = "Tools to manipulate font files"
|
| 342 |
optional = false
|
| 343 |
python-versions = ">=3.9"
|
| 344 |
groups = ["main"]
|
| 345 |
files = [
|
| 346 |
+
{file = "fonttools-4.58.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d500d399aa4e92d969a0d21052696fa762385bb23c3e733703af4a195ad9f34c"},
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| 347 |
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| 348 |
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{file = "fonttools-4.58.5-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:c5579fb3744dfec151b5c29b35857df83e01f06fe446e8c2ebaf1effd7e6cdce"},
|
| 349 |
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| 350 |
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{file = "fonttools-4.58.5-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:a81769fc4d473c808310c9ed91fbe01b67f615e3196fb9773e093939f59e6783"},
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| 351 |
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| 353 |
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| 354 |
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| 360 |
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| 361 |
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| 363 |
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| 364 |
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| 365 |
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| 375 |
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| 377 |
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| 378 |
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| 380 |
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| 381 |
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| 385 |
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| 388 |
]
|
| 389 |
|
| 390 |
[package.extras]
|
|
|
|
| 443 |
|
| 444 |
[[package]]
|
| 445 |
name = "grpcio"
|
| 446 |
+
version = "1.73.1"
|
| 447 |
description = "HTTP/2-based RPC framework"
|
| 448 |
optional = false
|
| 449 |
python-versions = ">=3.9"
|
| 450 |
groups = ["main"]
|
| 451 |
files = [
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| 452 |
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{file = "grpcio-1.73.1-cp310-cp310-linux_armv7l.whl", hash = "sha256:2d70f4ddd0a823436c2624640570ed6097e40935c9194482475fe8e3d9754d55"},
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| 1891 |
+
{file = "scipy-1.16.0-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:7dcf42c380e1e3737b343dec21095c9a9ad3f9cbe06f9c05830b44b1786c9e90"},
|
| 1892 |
+
{file = "scipy-1.16.0-cp312-cp312-macosx_14_0_x86_64.whl", hash = "sha256:26ec28675f4a9d41587266084c626b02899db373717d9312fa96ab17ca1ae94d"},
|
| 1893 |
+
{file = "scipy-1.16.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:952358b7e58bd3197cfbd2f2f2ba829f258404bdf5db59514b515a8fe7a36c52"},
|
| 1894 |
+
{file = "scipy-1.16.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:03931b4e870c6fef5b5c0970d52c9f6ddd8c8d3e934a98f09308377eba6f3824"},
|
| 1895 |
+
{file = "scipy-1.16.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:512c4f4f85912767c351a0306824ccca6fd91307a9f4318efe8fdbd9d30562ef"},
|
| 1896 |
+
{file = "scipy-1.16.0-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:e69f798847e9add03d512eaf5081a9a5c9a98757d12e52e6186ed9681247a1ac"},
|
| 1897 |
+
{file = "scipy-1.16.0-cp312-cp312-win_amd64.whl", hash = "sha256:adf9b1999323ba335adc5d1dc7add4781cb5a4b0ef1e98b79768c05c796c4e49"},
|
| 1898 |
+
{file = "scipy-1.16.0-cp313-cp313-macosx_10_14_x86_64.whl", hash = "sha256:e9f414cbe9ca289a73e0cc92e33a6a791469b6619c240aa32ee18abdce8ab451"},
|
| 1899 |
+
{file = "scipy-1.16.0-cp313-cp313-macosx_12_0_arm64.whl", hash = "sha256:bbba55fb97ba3cdef9b1ee973f06b09d518c0c7c66a009c729c7d1592be1935e"},
|
| 1900 |
+
{file = "scipy-1.16.0-cp313-cp313-macosx_14_0_arm64.whl", hash = "sha256:58e0d4354eacb6004e7aa1cd350e5514bd0270acaa8d5b36c0627bb3bb486974"},
|
| 1901 |
+
{file = "scipy-1.16.0-cp313-cp313-macosx_14_0_x86_64.whl", hash = "sha256:75b2094ec975c80efc273567436e16bb794660509c12c6a31eb5c195cbf4b6dc"},
|
| 1902 |
+
{file = "scipy-1.16.0-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:6b65d232157a380fdd11a560e7e21cde34fdb69d65c09cb87f6cc024ee376351"},
|
| 1903 |
+
{file = "scipy-1.16.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:1d8747f7736accd39289943f7fe53a8333be7f15a82eea08e4afe47d79568c32"},
|
| 1904 |
+
{file = "scipy-1.16.0-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:eb9f147a1b8529bb7fec2a85cf4cf42bdfadf9e83535c309a11fdae598c88e8b"},
|
| 1905 |
+
{file = "scipy-1.16.0-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:d2b83c37edbfa837a8923d19c749c1935ad3d41cf196006a24ed44dba2ec4358"},
|
| 1906 |
+
{file = "scipy-1.16.0-cp313-cp313-win_amd64.whl", hash = "sha256:79a3c13d43c95aa80b87328a46031cf52508cf5f4df2767602c984ed1d3c6bbe"},
|
| 1907 |
+
{file = "scipy-1.16.0-cp313-cp313t-macosx_10_14_x86_64.whl", hash = "sha256:f91b87e1689f0370690e8470916fe1b2308e5b2061317ff76977c8f836452a47"},
|
| 1908 |
+
{file = "scipy-1.16.0-cp313-cp313t-macosx_12_0_arm64.whl", hash = "sha256:88a6ca658fb94640079e7a50b2ad3b67e33ef0f40e70bdb7dc22017dae73ac08"},
|
| 1909 |
+
{file = "scipy-1.16.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:ae902626972f1bd7e4e86f58fd72322d7f4ec7b0cfc17b15d4b7006efc385176"},
|
| 1910 |
+
{file = "scipy-1.16.0-cp313-cp313t-macosx_14_0_x86_64.whl", hash = "sha256:8cb824c1fc75ef29893bc32b3ddd7b11cf9ab13c1127fe26413a05953b8c32ed"},
|
| 1911 |
+
{file = "scipy-1.16.0-cp313-cp313t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:de2db7250ff6514366a9709c2cba35cb6d08498e961cba20d7cff98a7ee88938"},
|
| 1912 |
+
{file = "scipy-1.16.0-cp313-cp313t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:e85800274edf4db8dd2e4e93034f92d1b05c9421220e7ded9988b16976f849c1"},
|
| 1913 |
+
{file = "scipy-1.16.0-cp313-cp313t-musllinux_1_2_aarch64.whl", hash = "sha256:4f720300a3024c237ace1cb11f9a84c38beb19616ba7c4cdcd771047a10a1706"},
|
| 1914 |
+
{file = "scipy-1.16.0-cp313-cp313t-musllinux_1_2_x86_64.whl", hash = "sha256:aad603e9339ddb676409b104c48a027e9916ce0d2838830691f39552b38a352e"},
|
| 1915 |
+
{file = "scipy-1.16.0-cp313-cp313t-win_amd64.whl", hash = "sha256:f56296fefca67ba605fd74d12f7bd23636267731a72cb3947963e76b8c0a25db"},
|
| 1916 |
+
{file = "scipy-1.16.0.tar.gz", hash = "sha256:b5ef54021e832869c8cfb03bc3bf20366cbcd426e02a58e8a58d7584dfbb8f62"},
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1917 |
]
|
| 1918 |
|
| 1919 |
[package.dependencies]
|
| 1920 |
+
numpy = ">=1.25.2,<2.6"
|
| 1921 |
|
| 1922 |
[package.extras]
|
| 1923 |
dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
|
| 1924 |
+
doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "linkify-it-py", "matplotlib (>=3.5)", "myst-nb (>=1.2.0)", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.2.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
|
| 1925 |
+
test = ["Cython", "array-api-strict (>=2.3.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
|
| 1926 |
|
| 1927 |
[[package]]
|
| 1928 |
name = "setuptools"
|
|
|
|
| 2147 |
|
| 2148 |
[[package]]
|
| 2149 |
name = "torchio"
|
| 2150 |
+
version = "0.20.17"
|
| 2151 |
description = "Tools for medical image processing with PyTorch"
|
| 2152 |
optional = false
|
| 2153 |
python-versions = ">=3.9"
|
| 2154 |
groups = ["main"]
|
| 2155 |
files = [
|
| 2156 |
+
{file = "torchio-0.20.17-py3-none-any.whl", hash = "sha256:3f08201e2523a721036a45cd72a51a3792078a38101ec7cce3280f344e98cc38"},
|
| 2157 |
+
{file = "torchio-0.20.17.tar.gz", hash = "sha256:559a87a56753ed08ac19546ded31a75a59f7af58689672592c13878ddef37d40"},
|
| 2158 |
]
|
| 2159 |
|
| 2160 |
[package.dependencies]
|
|
|
|
| 2285 |
|
| 2286 |
[[package]]
|
| 2287 |
name = "typing-extensions"
|
| 2288 |
+
version = "4.14.1"
|
| 2289 |
description = "Backported and Experimental Type Hints for Python 3.9+"
|
| 2290 |
optional = false
|
| 2291 |
python-versions = ">=3.9"
|
| 2292 |
groups = ["main"]
|
| 2293 |
files = [
|
| 2294 |
+
{file = "typing_extensions-4.14.1-py3-none-any.whl", hash = "sha256:d1e1e3b58374dc93031d6eda2420a48ea44a36c2b4766a4fdeb3710755731d76"},
|
| 2295 |
+
{file = "typing_extensions-4.14.1.tar.gz", hash = "sha256:38b39f4aeeab64884ce9f74c94263ef78f3c22467c8724005483154c26648d36"},
|
| 2296 |
]
|
| 2297 |
|
| 2298 |
[[package]]
|
|
|
|
| 2451 |
[metadata]
|
| 2452 |
lock-version = "2.1"
|
| 2453 |
python-versions = ">=3.12"
|
| 2454 |
+
content-hash = "ddcc47935dfc0f0ac6e87502c71233a58d421c5686411e1c26fc8f8ab36a405e"
|
pyproject.toml
CHANGED
|
@@ -12,10 +12,10 @@ license-files = [
|
|
| 12 |
readme = "README.md"
|
| 13 |
requires-python = ">=3.12"
|
| 14 |
dependencies = [
|
|
|
|
| 15 |
]
|
| 16 |
|
| 17 |
[tool.poetry.dependencies]
|
| 18 |
-
fastsurfer = { git = "https://github.com/Deep-MI/FastSurfer.git", rev = "stable" }
|
| 19 |
|
| 20 |
[build-system]
|
| 21 |
requires = ["poetry-core>=2.0.0,<3.0.0"]
|
|
|
|
| 12 |
readme = "README.md"
|
| 13 |
requires-python = ">=3.12"
|
| 14 |
dependencies = [
|
| 15 |
+
"fastsurfer @ file:///home/esten/repos/FastSurfer"
|
| 16 |
]
|
| 17 |
|
| 18 |
[tool.poetry.dependencies]
|
|
|
|
| 19 |
|
| 20 |
[build-system]
|
| 21 |
requires = ["poetry-core>=2.0.0,<3.0.0"]
|
scripts/preprocess.py
DELETED
|
@@ -1,20 +0,0 @@
|
|
| 1 |
-
import argparse
|
| 2 |
-
|
| 3 |
-
from FastSurferCNN.run_prediction import main
|
| 4 |
-
|
| 5 |
-
|
| 6 |
-
def preprocess(source_path: str, destination_path: str):
|
| 7 |
-
pass
|
| 8 |
-
|
| 9 |
-
if __name__ == "__main__":
|
| 10 |
-
parser = argparse.ArgumentParser(
|
| 11 |
-
'Preprocesses a given MRI image with FastSurfer'
|
| 12 |
-
)
|
| 13 |
-
parser.add_argument('-i', '--input', type=str, required=True,
|
| 14 |
-
help='Path to the MRI image to preprocess')
|
| 15 |
-
parser.add_argument('-o', '--output', type=str, required=True,
|
| 16 |
-
help='Path where the preprocessed image will be saved')
|
| 17 |
-
|
| 18 |
-
args = parser.parse_args()
|
| 19 |
-
|
| 20 |
-
preprocess(args.input, args.output)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
scripts/preprocess.sh
ADDED
|
@@ -0,0 +1,103 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/sh
|
| 2 |
+
|
| 3 |
+
echo "$PYTHONPATH"
|
| 4 |
+
|
| 5 |
+
# Function to display usage information
|
| 6 |
+
usage() {
|
| 7 |
+
echo "Usage: $0 --license LICENSE --python PYTHON INPUT OUTPUT"
|
| 8 |
+
echo "Arguments:"
|
| 9 |
+
echo " -l, --license LICENSE Path to FreeSurfer license (required)"
|
| 10 |
+
echo " -p, --python PYTHON Path to Python-executable to use (required)"
|
| 11 |
+
echo " INPUT Input file (required)"
|
| 12 |
+
echo " OUTPUT Output file (required)"
|
| 13 |
+
}
|
| 14 |
+
|
| 15 |
+
# Initialize variables
|
| 16 |
+
LICENSE=""
|
| 17 |
+
PYTHON=""
|
| 18 |
+
INPUT=""
|
| 19 |
+
OUTPUT=""
|
| 20 |
+
|
| 21 |
+
# Parse command line arguments
|
| 22 |
+
while [ $# -gt 0 ]; do
|
| 23 |
+
case $1 in
|
| 24 |
+
-l|--license)
|
| 25 |
+
LICENSE="$2"
|
| 26 |
+
shift 2
|
| 27 |
+
;;
|
| 28 |
+
-p|--python)
|
| 29 |
+
PYTHON="$2"
|
| 30 |
+
shift 2
|
| 31 |
+
;;
|
| 32 |
+
-*|--*)
|
| 33 |
+
echo "Unknown option $1"
|
| 34 |
+
exit 1
|
| 35 |
+
;;
|
| 36 |
+
*)
|
| 37 |
+
# Store positional arguments
|
| 38 |
+
if [ -z "$INPUT" ]; then
|
| 39 |
+
INPUT="$1"
|
| 40 |
+
elif [ -z "$OUTPUT" ]; then
|
| 41 |
+
OUTPUT="$1"
|
| 42 |
+
else
|
| 43 |
+
echo "Error: Too many positional arguments"
|
| 44 |
+
usage
|
| 45 |
+
exit 1
|
| 46 |
+
fi
|
| 47 |
+
shift
|
| 48 |
+
;;
|
| 49 |
+
esac
|
| 50 |
+
done
|
| 51 |
+
|
| 52 |
+
# Validate that exactly two positional arguments are provided
|
| 53 |
+
if [ -z "$INPUT" ] || [ -z "$OUTPUT" ]; then
|
| 54 |
+
echo "Error: This script requires exactly two arguments: INPUT and OUTPUT"
|
| 55 |
+
usage
|
| 56 |
+
exit 1
|
| 57 |
+
fi
|
| 58 |
+
|
| 59 |
+
# Validate that license is provided
|
| 60 |
+
if [ -z "$LICENSE" ]; then
|
| 61 |
+
echo "Error: License is required"
|
| 62 |
+
usage
|
| 63 |
+
exit 1
|
| 64 |
+
fi
|
| 65 |
+
if [ -z "$PYTHON" ]; then
|
| 66 |
+
echo "Error: Python is required"
|
| 67 |
+
usage
|
| 68 |
+
exit 1
|
| 69 |
+
fi
|
| 70 |
+
|
| 71 |
+
if [ ! -d "$INPUT" ]; then
|
| 72 |
+
echo "Error: Input directory '$INPUT' does not exist"
|
| 73 |
+
exit 1
|
| 74 |
+
fi
|
| 75 |
+
|
| 76 |
+
NIFTI_FILES=$(find "$INPUT" -name "*.nii.gz" -type f)
|
| 77 |
+
echo "Found $(echo "$NIFTI_FILES" | wc -l) .nii.gz files"
|
| 78 |
+
|
| 79 |
+
# Extract unique filenames and check for duplicates
|
| 80 |
+
UNIQUE_FILENAMES=$(echo "$NIFTI_FILES" | xargs -n1 basename | sort | uniq)
|
| 81 |
+
FILENAME_COUNT=$(echo "$UNIQUE_FILENAMES" | wc -l)
|
| 82 |
+
TOTAL_COUNT=$(echo "$NIFTI_FILES" | wc -l)
|
| 83 |
+
|
| 84 |
+
if [ "$FILENAME_COUNT" -ne "$TOTAL_COUNT" ]; then
|
| 85 |
+
echo "Error: Duplicate filenames detected!"
|
| 86 |
+
echo "Duplicate filenames:"
|
| 87 |
+
echo "$NIFTI_FILES" | xargs -n1 basename | sort | uniq -d
|
| 88 |
+
exit 1
|
| 89 |
+
fi
|
| 90 |
+
|
| 91 |
+
# Loop through each NIFTI file path
|
| 92 |
+
echo "$NIFTI_FILES" | while IFS= read -r filepath; do
|
| 93 |
+
# Extract filename without .nii.gz suffix
|
| 94 |
+
IMAGE=$(basename "$filepath" .nii.gz)
|
| 95 |
+
$FASTSURFER_HOME/run_fastsurfer.sh \
|
| 96 |
+
--sd $OUTPUT \
|
| 97 |
+
--sid $IMAGE \
|
| 98 |
+
--t1 $filepath \
|
| 99 |
+
--fs_license $LICENSE \
|
| 100 |
+
--py $PYTHON \
|
| 101 |
+
--seg_only
|
| 102 |
+
done
|
| 103 |
+
|