Build DSI Studio #449
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| name: Build DSI Studio | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| tag: | |
| description: 'Tag' | |
| required: true | |
| default: '2024.06.12' | |
| release_name: | |
| description: 'Release Name' | |
| required: true | |
| default: '2024 "Hou" Release' | |
| build_windows: | |
| type: boolean | |
| description: 'Build Windows' | |
| required: false | |
| default: 'true' | |
| build_linux: | |
| type: boolean | |
| description: 'Build Linux' | |
| required: false | |
| default: 'true' | |
| build_mac: | |
| type: boolean | |
| description: 'Build Mac' | |
| required: false | |
| default: 'true' | |
| build_docker: | |
| type: boolean | |
| description: 'Build Docker' | |
| required: false | |
| default: 'true' | |
| jobs: | |
| linux-build: | |
| if: ${{ github.event.inputs.build_linux == 'true' }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu2204,ubuntu2004,ubuntu1804,ubuntu1604,centos7] | |
| fail-fast: false | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.1 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3.0.0 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3.0.0 | |
| - name: Build and push | |
| uses: docker/build-push-action@v5.1.0 | |
| with: | |
| context: . | |
| file: build_packages/${{ matrix.os }}/Dockerfile | |
| push: false | |
| outputs: dsi-studio | |
| - name: Packaging | |
| run: | | |
| zip -r dsi_studio_${{ matrix.os }}.zip dsi-studio | |
| - name: Create Release | |
| uses: ncipollo/release-action@v1.13.0 | |
| with: | |
| allowUpdates: true | |
| artifacts: "*.zip" | |
| tag: ${{ github.event.inputs.tag }} | |
| name: ${{ github.event.inputs.release_name }} | |
| prerelease: false | |
| macos-build-qt5: | |
| if: ${{ github.event.inputs.build_mac == 'true' }} | |
| strategy: | |
| matrix: | |
| os: [macos-12] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| CFLAGS: -Werror | |
| steps: | |
| - uses: actions/checkout@v4.1.1 | |
| - name: Install Qt | |
| uses: jurplel/install-qt-action@v3.3.0 | |
| with: | |
| modules: qtcharts | |
| - name: Download TIPL and Atlases | |
| run: | | |
| git clone https://github.com/frankyeh/TIPL.git | |
| git clone https://github.com/frankyeh/DSI-Studio-atlas.git | |
| git clone https://github.com/frankyeh/UNet-Studio-Data.git | |
| rm -fr DSI-Studio-atlas/.git | |
| - name: Build DSI Studio | |
| run: | | |
| mkdir -p build | |
| cd build | |
| export PATH="$Qt5_DIR/bin:$PATH" && export LDFLAGS="-L$Qt5_DIR/lib" && export CPPFLAGS="-I$Qt5_DIR/include" && export PKG_CONFIG_PATH="$Qt5_DIR/lib/pkgconfig" | |
| qmake ../dsi_studio.pro DEFINES+="QMAKE_DEFAULT_INCDIRS=/usr/include QMAKE_DEFAULT_LIBDIRS=/usr/lib" | |
| make | |
| cd .. | |
| - name: Packaging | |
| run: | | |
| mv build/dsi_studio.app . | |
| macdeployqt dsi_studio.app | |
| curl -sSLO "https://github.com/frankyeh/TinyFSL/releases/download/2022.08.03/tiny_fsl_${{ matrix.os }}.zip" | |
| 7z e tiny_fsl_${{ matrix.os }}.zip -odsi_studio.app/Contents/MacOS/plugin | |
| rm -fr dsi_studio.app/Contents/MacOS/plugin/tiny_fsl | |
| rm *.zip | |
| mv other/* dsi_studio.app/Contents/MacOS/ | |
| mv DSI-Studio-atlas dsi_studio.app/Contents/MacOS/atlas | |
| mv UNet-Studio-Data/network dsi_studio.app/Contents/MacOS/ | |
| mv dsi_studio.icns dsi_studio.app/Contents/Resources/ | |
| zip -r dsi_studio_${{ matrix.os }}.zip dsi_studio.app | |
| - name: Create Release | |
| uses: ncipollo/release-action@v1.13.0 | |
| with: | |
| allowUpdates: true | |
| artifacts: "*.zip" | |
| tag: ${{ github.event.inputs.tag }} | |
| name: ${{ github.event.inputs.release_name }} | |
| prerelease: false | |
| macos-build-qt6: | |
| if: ${{ github.event.inputs.build_mac == 'true' }} | |
| strategy: | |
| matrix: | |
| os: [macos-13,macos-12] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| CFLAGS: -Werror | |
| steps: | |
| - uses: actions/checkout@v4.1.1 | |
| - name: brew update | |
| run: | | |
| brew update | |
| brew install cmake | |
| - name: Install Qt | |
| uses: jurplel/install-qt-action@v3.3.0 | |
| with: | |
| version: '6.5.2' | |
| modules: qtcharts | |
| - name: Download TIPL and Atlases | |
| run: | | |
| git clone https://github.com/frankyeh/TIPL.git | |
| git clone https://github.com/frankyeh/DSI-Studio-atlas.git | |
| git clone https://github.com/frankyeh/UNet-Studio-Data.git | |
| rm -fr DSI-Studio-atlas/.git | |
| - name: Build DSI Studio | |
| run: | | |
| mkdir -p build | |
| cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release -DTIPL_DIR=. | |
| cmake --build ./build --parallel --config Release | |
| - name: Packaging | |
| run: | | |
| mv build/dsi_studio.app . | |
| macdeployqt dsi_studio.app | |
| curl -sSLO "https://github.com/frankyeh/TinyFSL/releases/download/2022.08.03/tiny_fsl_${{ matrix.os }}.zip" | |
| 7z e tiny_fsl_${{ matrix.os }}.zip -odsi_studio.app/Contents/MacOS/plugin | |
| rm -fr dsi_studio.app/Contents/MacOS/plugin/tiny_fsl | |
| rm *.zip | |
| mv other/* dsi_studio.app/Contents/MacOS/ | |
| mv DSI-Studio-atlas dsi_studio.app/Contents/MacOS/atlas | |
| mv UNet-Studio-Data/network dsi_studio.app/Contents/MacOS/ | |
| mv dsi_studio.icns dsi_studio.app/Contents/Resources/ | |
| zip -r dsi_studio_${{ matrix.os }}_qt6.zip dsi_studio.app | |
| - name: Create Release | |
| uses: ncipollo/release-action@v1.13.0 | |
| with: | |
| allowUpdates: true | |
| artifacts: "*.zip" | |
| tag: ${{ github.event.inputs.tag }} | |
| name: ${{ github.event.inputs.release_name }} | |
| prerelease: false | |
| windows_build: | |
| if: ${{ github.event.inputs.build_windows == 'true' }} | |
| runs-on: windows-2019 | |
| steps: | |
| - uses: actions/checkout@v4.1.1 | |
| - name: Install Qt | |
| uses: jurplel/install-qt-action@v3.2.1 | |
| with: | |
| version: 6.5.2 | |
| modules: addons.qtcharts | |
| - name: Step to run when failed | |
| if: ${{ failure() }} | |
| uses: jurplel/install-qt-action@v3.2.1 | |
| with: | |
| version: 6.5.2 | |
| modules: addons.qtcharts | |
| - name: Install Ninja and CMake | |
| run: | | |
| choco install ninja cmake | |
| - name: Install Zlib | |
| run: | | |
| ./build_packages/install_zlib.bat | |
| del "C:/Program Files/zlib/lib/zlib.lib" | |
| del "C:/Program Files/zlib/bin/zlib.dll" | |
| - name: get TIPL and DSI Studio atlas | |
| run: | | |
| git clone https://github.com/frankyeh/TIPL.git | |
| git clone https://github.com/frankyeh/DSI-Studio-atlas.git | |
| git clone https://github.com/frankyeh/UNet-Studio-Data.git | |
| - name: Build DSI Studio CPU | |
| run: | | |
| for /f "usebackq delims=#" %%a in (`"%programfiles(x86)%\Microsoft Visual Studio\Installer\vswhere" -latest -property installationPath`) do call "%%a\Common7\Tools\VsDevCmd.bat" -arch=x64 | |
| mkdir -p build_cpu | |
| cmake -S . -B build_cpu -GNinja "-DZLIB_LIBRARY=C:/Program Files/zlib/lib/zlibstatic.lib" "-DCMAKE_BUILD_TYPE:STRING=Release" "-DCMAKE_C_COMPILER:STRING=cl" "-DCMAKE_CXX_COMPILER:STRING=cl" -DTIPL_DIR=. | |
| cmake --build ./build_cpu --parallel --config Release | |
| shell: cmd | |
| - name: Install Cuda | |
| uses: Jimver/cuda-toolkit@v0.2.11 | |
| - name: Build DSI Studio | |
| run: | | |
| for /f "usebackq delims=#" %%a in (`"%programfiles(x86)%\Microsoft Visual Studio\Installer\vswhere" -latest -property installationPath`) do call "%%a\Common7\Tools\VsDevCmd.bat" -arch=x64 | |
| mkdir -p build | |
| cmake -S . -B build -GNinja "-DZLIB_LIBRARY=C:/Program Files/zlib/lib/zlibstatic.lib" "-DCMAKE_BUILD_TYPE:STRING=Release" "-DCMAKE_C_COMPILER:STRING=cl" "-DCMAKE_CXX_COMPILER:STRING=cl" -DTIPL_DIR=. | |
| cmake --build ./build --parallel --config Release | |
| shell: cmd | |
| - name: Packaging | |
| run: | | |
| mkdir dsi_studio_win | |
| move other\color_map dsi_studio_win | |
| move other\* dsi_studio_win | |
| move build\dsi_studio.exe dsi_studio_win | |
| windeployqt --no-translations --no-system-d3d-compiler --compiler-runtime --no-opengl-sw dsi_studio_win\dsi_studio.exe | |
| move DSI-Studio-atlas dsi_studio_win\atlas | |
| rm dsi_studio_win\atlas\.git -r -force | |
| move UNet-Studio-Data\network dsi_studio_win\ | |
| curl -sSLO "https://github.com/frankyeh/TinyFSL/releases/download/2022.08.03/tiny_fsl_win.zip" | |
| 7z e tiny_fsl_win.zip -odsi_studio_win\plugin | |
| rm dsi_studio_win\plugin\cublas* | |
| rd dsi_studio_win\plugin\tiny_fsl | |
| del *.zip | |
| - name: Zip Release | |
| uses: TheDoctor0/zip-release@0.7.6 | |
| with: | |
| filename: dsi_studio_win.zip | |
| exclusions: .git | |
| path: dsi_studio_win | |
| - name: Packaging | |
| run: | | |
| rename dsi_studio_win dsi_studio_win_cpu | |
| move build_cpu\dsi_studio.exe dsi_studio_win_cpu | |
| windeployqt --no-translations --no-system-d3d-compiler --compiler-runtime --no-opengl-sw dsi_studio_win_cpu\dsi_studio.exe | |
| shell: cmd | |
| - name: Zip Release | |
| uses: TheDoctor0/zip-release@0.7.6 | |
| with: | |
| filename: dsi_studio_win_cpu.zip | |
| exclusions: .git | |
| path: dsi_studio_win_cpu | |
| - name: Create Release | |
| uses: ncipollo/release-action@v1.13.0 | |
| with: | |
| allowUpdates: true | |
| artifacts: "*.zip" | |
| tag: ${{ github.event.inputs.tag }} | |
| name: ${{ github.event.inputs.release_name }} | |
| prerelease: false | |
| docker_build: | |
| if: ${{ github.event.inputs.build_docker == 'true' }} | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4.1.1 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3.0.0 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3.0.0 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Login to the Container registry | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Current Time | |
| run: echo "DATE_TAG=$(date "+%Y-%m-%d")" >> $GITHUB_ENV | |
| - name: Build and push | |
| uses: docker/build-push-action@v5.1.0 | |
| with: | |
| context: . | |
| file: build_packages/docker/Dockerfile | |
| push: true | |
| tags: | | |
| "dsistudio/dsistudio:chen-${{ env.DATE_TAG }}" | |
| dsistudio/dsistudio:latest | |
| test_animal_recon: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6321169/files/mountsinai-S-sub-032156_dwi.src.gz?download=1 -o Rhesus.src.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Test DTI Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec --method=1 |& tee -a log.txt | |
| ls Rhesus.src.gz.dti.fib.gz | |
| - name: Test GQI Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec |& tee -a log.txt | |
| ls Rhesus.src.gz.gqi.1.25.fib.gz | |
| - name: Test QSDR Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec --method=7 |& tee -a log.txt | |
| ls Rhesus.src.gz.* | |
| test_human_recon: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6320992/files/20081006_M025Y_DSI_203.src.gz?download=1 -o DSI.src.gz | |
| curl -sL https://zenodo.org/record/6320992/files/20081006_M025Y_DTI64.src.gz?download=1 -o DTI.src.gz | |
| curl -sL https://zenodo.org/record/6320992/files/20081006_M025Y_HARDI.src.gz?download=1 -o HARDI.src.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Test DTI Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec --method=1 | |
| ls DSI.src.gz.dti.fib.gz | |
| ls DTI.src.gz.dti.fib.gz | |
| ls HARDI.src.gz.dti.fib.gz | |
| - name: Test GQI Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec | |
| ls DSI.src.gz.gqi.1.25.fib.gz | |
| ls DTI.src.gz.gqi.1.25.fib.gz | |
| ls HARDI.src.gz.gqi.1.25.fib.gz | |
| - name: Test QSDR Recon | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.src.gz --action=rec --method=7 --template=0 | |
| ls DSI.src.gz.icbm152_adult.qsdr.1.25.* | |
| ls DTI.src.gz.icbm152_adult.qsdr.1.25.* | |
| ls HARDI.src.gz.icbm152_adult.qsdr.1.25.* | |
| test_human_tracking_qsdr: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://github.com/frankyeh/DSI-Studio-atlas/blob/main/ICBM152_adult/ICBM152_adult.fib.gz?raw=true -o ICBM152_adult.fib.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Tracking | |
| run: | | |
| ./dsi-studio/dsi_studio --source=ICBM152_adult.fib.gz --action=trk --output=icbm152.tt.gz --export=stat,tdi | |
| ls icbm152.tt.gz | |
| ls icbm152.tt.gz.tdi.nii.gz | |
| ls icbm152.tt.gz.stat.txt | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=ICBM152_adult.fib.gz --action=trk --track_id=ArcuateFasciculusL --tip_iteration=0 --output=AF_L.tt.gz | |
| ls AF_L.tt.gz | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=ICBM152_adult.fib.gz --action=trk --roi=FreeSurferDKT_Cortical:left_precentral,dilate,dilate,smoothing --roi2=FreeSurferDKT_Cortical:right_precentral,dilate,dilate,smoothing --output=LR.tt.gz | |
| ls LR.tt.gz | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=ICBM152_adult.fib.gz --action=trk --fiber_count=1000000 --output=no_file --connectivity=FreeSurferDKT_Cortical --connectivity_value=count,qa | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.connectivity.mat | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.connectogram.txt | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.network_measures.txt | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.connectivity.mat | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.connectogram.txt | |
| ls ICBM152_adult.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.network_measures.txt | |
| test_human_tracking_gqi: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6307812/files/100206.src.gz.gqi.1.7.fib.gz?download=1 -o 100206.fib.gz | |
| curl -sL https://github.com/frankyeh/DSI-Studio-atlas/blob/main/ICBM152_adult/ICBM152_adult.QA.nii.gz?raw=true -o template_qa.nii.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Tracking | |
| run: | | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=trk --output=100206.tt.gz --export=stat,tdi | |
| ls 100206.tt.gz | |
| ls 100206.tt.gz.tdi.nii.gz | |
| ls 100206.tt.gz.stat.txt | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=trk --track_id=ArcuateFasciculusL --tip_iteration=0 --output=AF_L.tt.gz | |
| ls AF_L.tt.gz | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=trk --roi=FreeSurferDKT_Cortical:left_precentral,dilate,dilate,smoothing --roi2=FreeSurferDKT_Cortical:right_precentral,dilate,dilate,smoothing --output=LR.tt.gz | |
| ls LR.tt.gz | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=trk --fiber_count=1000000 --output=no_file --connectivity=FreeSurferDKT_Cortical --connectivity_value=count,qa | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.connectivity.mat | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.connectogram.txt | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.count.pass.network_measures.txt | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.connectivity.mat | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.connectogram.txt | |
| ls 100206.fib.gz.tt.gz.FreeSurferDKT_Cortical.qa.pass.network_measures.txt | |
| echo -------------------------------------------------------------------------------------------------- | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=trk --other_slices=template_qa.nii.gz --dt_threshold_index=template_qa-qa --seed_count=1000000 --dt_threshold=0.1 --output=dt.tt.gz | |
| ls dt.tt.gz | |
| test_export_registration: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6307812/files/100206.src.gz.gqi.1.7.fib.gz?download=1 -o 100206.fib.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Export | |
| run: | | |
| ./dsi-studio/dsi_studio --source=100206.fib.gz --action=exp --export=qa,iso | |
| ls 100206.fib.gz.qa.nii.gz | |
| ls 100206.fib.gz.iso.nii.gz | |
| - name: Registration | |
| run: | | |
| curl -sL https://zenodo.org/record/6324701/files/HCP1065_qa.nii.gz?download=1 -o HCP1065_qa.nii.gz | |
| curl -sL https://zenodo.org/record/6324701/files/HCP1065_iso.nii.gz?download=1 -o HCP1065_iso.nii.gz | |
| ./dsi-studio/dsi_studio --action=reg --from=100206.fib.gz.qa.nii.gz --to=HCP1065_qa.nii.gz --apply_warp=100206.fib.gz.qa.nii.gz | |
| ls 100206.fib.gz.qa.nii.gz.wp.nii.gz | |
| ./dsi-studio/dsi_studio --action=reg --from=100206.fib.gz.qa.nii.gz --to=HCP1065_qa.nii.gz --from2=100206.fib.gz.iso.nii.gz --to2=HCP1065_iso.nii.gz --apply_warp=100206.fib.gz.qa.nii.gz | |
| ls 100206.fib.gz.qa.nii.gz.wp.nii.gz | |
| test_connectometry: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6324701/files/CMU60.db.fib.gz?download=1 -o CMU60.db.fib.gz | |
| curl -sL https://zenodo.org/record/6324701/files/CMU60.demo.csv?download=1 -o CMU60.demo.csv | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Connectometry | |
| run: | | |
| ./dsi-studio/dsi_studio --source=CMU60.db.fib.gz --action=cnt --demo=CMU60.demo.csv --t_threshold=2.5 --permutation=200 --variable_list=0,1,2 --voi=1 | |
| ls *.report.html | |
| ls * -l | |
| test_automatic_tracking: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| curl -sL https://zenodo.org/record/6307812/files/100206.src.gz.gqi.1.7.fib.gz?download=1 -o 100206.fib.gz | |
| curl -sL https://zenodo.org/record/6307812/files/100307.src.gz.gqi.1.7.fib.gz?download=1 -o 100307.fib.gz | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Tracking | |
| run: | | |
| ./dsi-studio/dsi_studio --source=*.fib.gz --action=atk --track_id=ArcuateFasciculusL | |
| ls */*ArcuateFasciculusL.tt.gz | |
| test_src_construction: | |
| needs: linux-build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Setup Environment | |
| run: | | |
| curl -sL "https://github.com/frankyeh/DSI-Studio/releases/download/${{ github.event.inputs.tag }}/dsi_studio_ubuntu2004.zip" | jar x | |
| chmod 777 ./dsi-studio/dsi_studio | |
| - name: Test GQI Recon | |
| run: | | |
| aws s3 sync --no-sign-request --region eu-west-1 --exclude "*" --include "*dwi.*" s3://openneuro.org/ds002087 ds002087 | |
| ./dsi-studio/dsi_studio --action=src --source=ds002087 |