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Jul 15, 2025
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Dockerfile for PET2BIDS #359

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Dockerfile for PET2BIDS
ramroomh Jul 11, 2025
5703789
Updated ReadMe with docker usage
ramroomh Jul 15, 2025
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39 changes: 39 additions & 0 deletions Dockerfile
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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
3 changes: 2 additions & 1 deletion contributors.md
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Expand Up @@ -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 💻 💬 🤔 ⚠️ 👀
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21 changes: 20 additions & 1 deletion pypet2bids/README.md
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Expand Up @@ -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
Expand All @@ -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
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