crashs 0.2.0__tar.gz

crashs-0.2.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

crashs-0.2.0/.gitignore

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+# For this project
+tmp
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.*~
+.DS_Store

crashs-0.2.0/Dockerfile

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+# THE FIRST PART OF THIS Dockerfile is taken from https://github.com/nighres/nighres/blob/master/Dockerfile
+# Start from the official Debian image
+FROM debian:bullseye
+
+<<<<<<< Updated upstream
+# Install nighres prerequisites
+RUN echo "deb http://archive.ubuntu.com/ubuntu/ bionic main universe" >> /etc/apt/sources.list
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3B4FE6ACC0B21F32
+RUN apt-get update
+RUN apt-get install -y openjdk-11-jdk python3-jcc
+
+# Install nighres
+RUN git clone https://github.com/nighres/nighres /tk/nighres && cd /tk/nighres && git checkout 7293c368476a015708b3a89c43409fdfdef9e19c
+RUN ln -s /usr/lib/jvm/java-11-openjdk-amd64 /usr/lib/jvm/default-java
+RUN apt-get install -y wget
+WORKDIR /tk/nighres
+RUN ./build.sh || ./build.sh
+RUN python3 -m pip install .
+RUN pip3 install nibabel==3.2.2
+=======
+# Install necessary tools and dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    git \
+    build-essential \
+    python3 \
+    python3-pip \
+    python3-dev \
+    libffi-dev \
+    openjdk-17-jdk \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+
+# Adjust JAVA_HOME if necessary and create a symbolic link to match JCC's expected JDK path
+# RUN ls -l /usr/lib/jvm && exit 255
+ENV JAVA_HOME=/usr/lib/jvm/openjdk-17
+RUN ln -s $JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
+
+# Install JCC
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install jcc
+
+# Clone the nighres repository
+RUN git clone https://github.com/nighres/nighres
+
+# Change directory into the 	cloned repository, run the build script, and install nighres
+WORKDIR /nighres
+RUN ./build.sh && \
+    python3 -m pip install .
+
+# Install nighres
+#RUN git clone https://github.com/nighres/nighres /tk/nighres && cd /tk/nighres && git checkout master
+#RUN ln -s /usr/lib/jvm/java-11-openjdk-amd64 /usr/lib/jvm/default-java
+#RUN apt-get install -y wget
+#WORKDIR /tk/nighres
+#RUN ./build.sh || ./build.sh
+#RUN python3 -m pip install .
+#RUN pip3 install nibabel==3.2.2
+>>>>>>> Stashed changes
+
+# Install python packages
+COPY ./requirements.txt /tmp/
+RUN pip install -r /tmp/requirements.txt
+
+# Copy the contents
+COPY . /tk/crashs
+WORKDIR /tk/crashs

crashs-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Paul Yushkevich
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

crashs-0.2.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: crashs
+Version: 0.2.0
+Summary: CRASHS: Cortical Reconstruction for Automated Segmentation of Hippocampal Subfields (ASHS)
+Project-URL: Homepage, https://github.com/pyushkevich/crashs
+Author-email: Paul Yushkevich <pyushkevich@gmail.com>
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# crashs=Cruise+ASHS
+CRASHS is a surface-based modeling and groupwise registration pipeline for the human medial temporal lobe (MTL). It is used to postprocess the results of [ASHS](https://github.com/pyushkevich/ashs) segmentation with ASHS atlases that contain a white matter label. CRASHS uses the [CRUISE](https://doi.org/10.1016/j.neuroimage.2004.06.043) technique implemented in the [NighRes software](https://nighres.readthedocs.io/en/latest/) to fit the white matter segmentation with a surface of spherical topology, and find a series of surfaces spanning between the gray/white boundary and the pial surface. The middle surface is inflated and registered to a population template, allowing surface-based analysis of MTL cortical thickness and other measures such as functional MRI and diffusion MRI. 
+
+## Inputs
+The main input to the package is the ASHS-T1 output folder. ASHS should be run using the new [ASHS-T1 atlas with the white matter label](https://www.nitrc.org/frs/downloadlink.php/13554).
+
+## Outputs
+The program generates many outputs, but the most useful ones are:
+* `fitting/[ID]_fitted_omt_hw_target.vtk`: the grey/white and grey/csf boundaries estimated by the `cruise_cortex_extraction` module of NighRes. These meshes are in physical (RAS) coordinate space, not in voxel (IJK) space output by Nighres. *If you extract meshes from the T1-ASHS segmentation in ITK-SNAP, those should like up with these meshes.*
+
+* `fitting/[ID]_fitted_omt_hw_target.vtk`: the mid-surface of the gray matter estimated by the `volumetric_layering` module of NighRes. Also in RAS space.
+
+* `fitting/[ID]_fitted_omt_match_to_hw.vtk`: the template mesh projected onto the mid-surface surface, also in RAS space. This should have the same geometry as the mid-surface, but the same number of vertices/faces as the template. This mesh will also have scalar arrays for the anatomical label and other features from the template, such as template curvature (useful for visualization). **This mesh can be used to map data from subject space (thickness, fMRI, NODDI, etc) into template space for group analysis**
+
+The following files can be used to check how well the fitting between the inflated template mid-surface and the inflated subject mid-surface worked.
+
+* `fitting/[ID]_fit_target_reduced`: this is the inflated and sub-sampled mid-surface mesh of the subject, affine transformed into the space of the inflated template. Each triangle is associated with an anatomical label.
+
+* `fitting/[ID]_fitted_lddmm_template`: this is the inflated template warped to optimally match the mesh above. The fit is not perfect but should be close.
+
+* `fitting/[ID]_fitted_dist_stat.json`: distance statistics of the fitting, including average, max, and 95th percentile of the distance. Useful to check for poor fitting results.
+
+
+## Docker
+This repository includes the CRASHS scripts and a `Dockerfile`. The official container on DockerHub is labeled `pyushkevich/crashs:latest`
+
+    docker run -v your_data_directory:/data -it pyushkevich/crashs:latest /bin/bash
+    ./crashs.py --help
+    
+A sample dataset is also provided and can be processed as follows (also see `run_sample.sh`)
+
+    docker run -v your_data_directory:/data -it pyushkevich/crashs:latest /bin/bash
+    ./crashs.py -s right -r 0.1 sample_data/035_S_4082_2011-06-28 templates/crashs_template_01 /data/test
+
+## Citation
+* PA Yushkevich, L Xie, LEM Wisse, M Dong, S Ravikumar, R Ittyerah,  R de Flores, SR Das, DA Wolk for the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Mapping Medial Temporal Lobe Longitudinal Change in Preclinical Alzheimer’s Disease, 2023 Alzheimer's Association International Conference (AAIC 2023).
+
+
+    

crashs-0.2.0/README.md

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+# crashs=Cruise+ASHS
+CRASHS is a surface-based modeling and groupwise registration pipeline for the human medial temporal lobe (MTL). It is used to postprocess the results of [ASHS](https://github.com/pyushkevich/ashs) segmentation with ASHS atlases that contain a white matter label. CRASHS uses the [CRUISE](https://doi.org/10.1016/j.neuroimage.2004.06.043) technique implemented in the [NighRes software](https://nighres.readthedocs.io/en/latest/) to fit the white matter segmentation with a surface of spherical topology, and find a series of surfaces spanning between the gray/white boundary and the pial surface. The middle surface is inflated and registered to a population template, allowing surface-based analysis of MTL cortical thickness and other measures such as functional MRI and diffusion MRI. 
+
+## Inputs
+The main input to the package is the ASHS-T1 output folder. ASHS should be run using the new [ASHS-T1 atlas with the white matter label](https://www.nitrc.org/frs/downloadlink.php/13554).
+
+## Outputs
+The program generates many outputs, but the most useful ones are:
+* `fitting/[ID]_fitted_omt_hw_target.vtk`: the grey/white and grey/csf boundaries estimated by the `cruise_cortex_extraction` module of NighRes. These meshes are in physical (RAS) coordinate space, not in voxel (IJK) space output by Nighres. *If you extract meshes from the T1-ASHS segmentation in ITK-SNAP, those should like up with these meshes.*
+
+* `fitting/[ID]_fitted_omt_hw_target.vtk`: the mid-surface of the gray matter estimated by the `volumetric_layering` module of NighRes. Also in RAS space.
+
+* `fitting/[ID]_fitted_omt_match_to_hw.vtk`: the template mesh projected onto the mid-surface surface, also in RAS space. This should have the same geometry as the mid-surface, but the same number of vertices/faces as the template. This mesh will also have scalar arrays for the anatomical label and other features from the template, such as template curvature (useful for visualization). **This mesh can be used to map data from subject space (thickness, fMRI, NODDI, etc) into template space for group analysis**
+
+The following files can be used to check how well the fitting between the inflated template mid-surface and the inflated subject mid-surface worked.
+
+* `fitting/[ID]_fit_target_reduced`: this is the inflated and sub-sampled mid-surface mesh of the subject, affine transformed into the space of the inflated template. Each triangle is associated with an anatomical label.
+
+* `fitting/[ID]_fitted_lddmm_template`: this is the inflated template warped to optimally match the mesh above. The fit is not perfect but should be close.
+
+* `fitting/[ID]_fitted_dist_stat.json`: distance statistics of the fitting, including average, max, and 95th percentile of the distance. Useful to check for poor fitting results.
+
+
+## Docker
+This repository includes the CRASHS scripts and a `Dockerfile`. The official container on DockerHub is labeled `pyushkevich/crashs:latest`
+
+    docker run -v your_data_directory:/data -it pyushkevich/crashs:latest /bin/bash
+    ./crashs.py --help
+    
+A sample dataset is also provided and can be processed as follows (also see `run_sample.sh`)
+
+    docker run -v your_data_directory:/data -it pyushkevich/crashs:latest /bin/bash
+    ./crashs.py -s right -r 0.1 sample_data/035_S_4082_2011-06-28 templates/crashs_template_01 /data/test
+
+## Citation
+* PA Yushkevich, L Xie, LEM Wisse, M Dong, S Ravikumar, R Ittyerah,  R de Flores, SR Das, DA Wolk for the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Mapping Medial Temporal Lobe Longitudinal Change in Preclinical Alzheimer’s Disease, 2023 Alzheimer's Association International Conference (AAIC 2023).
+
+
+