add dcm2niix binaries

.github/workflows/phantoms.yaml

@@ -27,7 +27,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
         python: ["3.12"]
       fail-fast: false
 
@@ -36,14 +36,14 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Cache Node Posix
-        if: runner.os != 'Windows' && !env.ACT
+        if: runner.os != 'Windows' && env.ACT != 'true'
         uses: actions/cache@v4
         with:
           path: ~/.npm
           key: npm-${{ runner.os }}-${{ env.cache-name }}
 
       - name: Cache Phantoms
-        if: ${{ !env.ACT }}
+        if: env.ACT != 'true'
         id: phantom-cache
         uses: actions/cache@v4
         env:
@@ -55,41 +55,21 @@ jobs:
             ${{ runner.os }}-${{ env.cache-name }}-
             ${{ runner.os }}- 
 
-      - name: Install dcm2niix posix
-        if: runner.os != 'Windows'
-        run: |
-          if [ "$RUNNER_OS" == "Linux" ]; then
-            mkdir dcm2niix_install/ && cd dcm2niix_install/
-            curl -fLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20230411/dcm2niix_lnx.zip
-            unzip dcm2niix*.zip
-            echo "${{ github.workspace }}/dcm2niix_install/" >> $GITHUB_PATH
-          elif [ "$RUNNER_OS" == "macOS" ]; then
-            brew install dcm2niix
-          fi
-
-
-      - name: Check dcm2niix is installed and on path
-        if: runner.os != 'Windows'
-        run:
-          dcm2niix -h 
-
-      - name: Install dcm2niix windows
-        if: runner.os == 'Windows'
-        run: |
-          curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_win.zip
-          powershell -command "Expand-Archive dcm2niix_win.zip"
-
       - name: Set up python
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
-          cache: 'pip'
-          cache-dependency-path: |
-            pypet2bids/pyproject.toml
 
-      - name: Install UV
+      - name: Install UV (Linux/macOS)
+        if: runner.os != 'Windows'
         run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH
 
+      - name: Install UV (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
+          echo "$env:USERPROFILE\.cargo\bin" >> $env:GITHUB_PATH
+
       - name: Install Python Dependencies
         run: |
           cd pypet2bids
@@ -108,30 +88,43 @@ jobs:
       - name: Install BIDS Validator
         run: npm install -g [email protected]
 
-      - name: Collect Phantoms
-        if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
+      - name: Collect Phantoms (Linux/macOS)
+        if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os != 'Windows'
         run: wget -O PHANTOMS.zip https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip
 
+      - name: Collect Phantoms (Windows)
+        if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os == 'Windows'
+        run: Invoke-WebRequest -Uri "https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip" -OutFile "PHANTOMS.zip"
+
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: github.event_name == 'workflow_dispatch' && inputs.debug_enabled
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
       - name: Decompress phantoms windows
         if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os == 'Windows'
-        run: powershell -command "Expand-Archive PHANTOMS.zip"
+        run: |
+          powershell -command "Expand-Archive PHANTOMS.zip"
+          # Move contents from PHANTOMS/OpenNeuroPET-Phantoms/ to OpenNeuroPET-Phantoms/
+          mv PHANTOMS/OpenNeuroPET-Phantoms .
 
       - name: Decompress phantoms posix
         if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os != 'Windows'
         run: unzip PHANTOMS.zip
 
-      - name: Copy Conversion Scripts from Version Control
+      - name: Copy Conversion Scripts from Version Control (Linux/macOS)
+        if: runner.os != 'Windows'
         run: |
           mkdir -p OpenNeuroPET-Phantoms/code/
           cp scripts/matlab_conversions.m OpenNeuroPET-Phantoms/code/matlab_conversions.m
           cp scripts/python_conversions.sh OpenNeuroPET-Phantoms/code/python_conversions.sh
 
-      - name: Debug
-        uses: mxschmitt/action-tmate@v3
-        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
-        timeout-minutes: 15
-        with:
-          limit-access-to-actor: true
+      - name: Copy Conversion Scripts from Version Control (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          cp scripts/python_conversions.sh OpenNeuroPET-Phantoms/code/python_conversions.sh
 
       - name: Run Python Conversion Script on Phantoms
         run: |
@@ -160,20 +153,16 @@ jobs:
             matlab_conversions
 
       - name: Check Parity
+        if: ${{ matrix.os == 'ubuntu-latest' }}
         run: |
           python scripts/compare_jsons.py OpenNeuroPET-Phantoms/python OpenNeuroPET-Phantoms/matlab
 
       - name: Validate Python Conversion
         run: |
           bids-validator OpenNeuroPET-Phantoms/python
 
-      - name: Debug
-        uses: mxschmitt/action-tmate@v3
-        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
-        timeout-minutes: 15
-        with:
-          limit-access-to-actor: true
 
       - name: Validate Matlab Conversion
+        if: ${{ matrix.os == 'ubuntu-latest'}}
         run: |
           bids-validator OpenNeuroPET-Phantoms/matlab

.github/workflows/test-included-binaries.yaml

@@ -0,0 +1,63 @@
+name: Test Included Binaries
+on:
+  push:
+    branches:
+      - main
+      - add-dcm2niix-binaries
+  pull_request:
+    branches:
+      - main
+      - add-dcm2niix-binaries
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run with tmate debugging enabled'
+        required: false
+        default: false
+
+jobs:
+  test-included-binaries:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: ['3.12']
+      fail-fast: false
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install UV
+        if: matrix.os != 'windows-latest'
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Install UV (Windows)
+        if: matrix.os == 'windows-latest'
+        run: |
+          powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
+          echo "$env:USERPROFILE\.cargo\bin" >> $env:GITHUB_PATH
+
+      - name: Install dependencies
+        run: |
+          cd pypet2bids
+          uv add --dev pytest
+          uv sync
+
+      - name: Debug Session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
+      - name: Run Tests
+        run: |
+          cd pypet2bids
+          uv run pytest tests/test_included_binaries.py -v

.gitignore

@@ -67,3 +67,5 @@ ecat_testing/**/*.nii*
 
 matlab/SiemensHRRTparameters.txt
 
+dcm2niix
+dcm2niix.exe

Dockerfile

@@ -0,0 +1,39 @@
+FROM python:3.11-slim
+
+LABEL maintainer="OpenNeuroPET team"
+LABEL description="PET2BIDS"
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    git \
+    curl \
+    wget \
+    unzip \
+    cmake \
+    build-essential \
+    pkg-config \
+    libturbojpeg0-dev \
+    libopenjp2-7-dev \
+    libjpeg-dev \
+    libcharls-dev \
+    zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /tmp
+# Build and install dcm2niix
+RUN git clone https://github.com/rordenlab/dcm2niix.git && \
+    cd dcm2niix && \
+    mkdir build && cd build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON .. && \
+    make && \
+    make install && \
+    ldconfig && \
+    cd / && rm -rf /tmp/dcm2niix
+
+# Verify dcm2niix installation and ensure it's in PATH
+RUN which dcm2niix && dcm2niix -h
+ENV PATH="/usr/local/bin:${PATH}"
+
+WORKDIR /out
+# Install pypet2bids
+RUN pip install pypet2bids

contributors.md

@@ -6,7 +6,8 @@ some icons needs to be added or your name is not listed, please add it.
 Murat Bilgel 💻 🐛 💡  
 Anthony Galassi 💻 📖 💬 🎨 💡 ⚠️  
 Melanie Ganz-Benjaminsen 🔍 💬 🤔 📋  
-Gabriel Gonzalez-Escamilla 💻 ⚠️ 🐛 👀  
+Gabriel Gonzalez-Escamilla 💻 ⚠️ 🐛 👀 
+Rami Hamati 💻 🐛 
 Gitte Knudsen 💡💵  
 Granville Matheson 📝 🐛 ✅  
 Martin Norgaard 💻 💬 🤔 ⚠️ 👀  

matlab/updatejsonpetfile.m

@@ -454,8 +454,13 @@
 for f = 1:length(shouldBarray)
     if isfield(filemetadata,shouldBarray{f})
         if isscalar(filemetadata.(shouldBarray{f}))
-            filemetadata.(shouldBarray{f}) = {filemetadata.(shouldBarray{f})};
-            updated = 1;
+            if ~iscell(filemetadata.(shouldBarray{f}))
+                filemetadata.(shouldBarray{f}) = {filemetadata.(shouldBarray{f})};
+                updated = 1;
+            elseif isnumeric(filemetadata.(shouldBarray{f}){1})
+                filemetadata.(shouldBarray{f}) = {filemetadata.(shouldBarray{f})};
+                updated = 1;
+            end
         elseif all(size(filemetadata.(shouldBarray{f})) == 1)
             if any(contains(filemetadata.(shouldBarray{f}),{'none'}))
                 filemetadata.(shouldBarray{f}) = {filemetadata.(shouldBarray{f})};

pypet2bids/README.md

@@ -77,7 +77,7 @@ make installpoetry buildpackage installpackage
 <details> 
 <summary>Run Directly From Source</summary>
 
-Lastly, if one wishes run pypet2bids directly from the source code in this repository or to help contribute to the python portion of this project or any of the documentation they can do so via the following options:
+If one wishes run pypet2bids directly from the source code in this repository or to help contribute to the python portion of this project or any of the documentation they can do so via the following options:
 
 ```bash
 cd PET2BIDS/pypet2bids
@@ -100,6 +100,25 @@ python dcm2niix4pet.py --help
 
 </details>
 
+<details>
+<summary>Run Using Docker</summary>
+Lastly, we provide a Docker container that includes dcm2niix and pypet2bids. This can be installed using Docker. To build the docker file run:
+
+```
+docker build . -t openneuropet/pet2bids
+```
+
+Then mount and run conversions on your input folders like so:
+
+```
+docker run --rm -it \ 
+-v /path/to/dicoms:/dicoms:ro \ 
+-v /path/to/outputdir:/out \ 
+openneuropet/pet2bids dcm2niix4pet /dicoms --destination-path /out
+```
+Please note the latest version of dcm2niix is pulled and installed at the time of building the Docker container.
+</details>
+
 **Note:**
 *We recommend using dcm2niix v1.0.20220720 or newer; we rely on metadata included in these later releases. It's best to 
 collect releases from the [rorden lab/dcm2niix/releases](https://github.com/rordenlab/dcm2niix/releases) page. We have