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chore: Begin streamlining Docker #84

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96104c1
Ignore dist/ to avoid polluting Docker build
effigies Aug 18, 2025
1571453
docker: Use uv build
effigies Aug 18, 2025
e56edee
docker: build-essential no longer needed
effigies Aug 18, 2025
82e1b66
chore: Remove unused FSL and AFNI tools
effigies Aug 18, 2025
0be540d
docker: Install petpvc from conda-forge
effigies Aug 19, 2025
e813e0f
chore: Upgrade requirements.txt with env.yml constraints
effigies Aug 19, 2025
9954412
env: Add fsl-avwutils for fslmerge, fslsplit
effigies Aug 19, 2025
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1 change: 1 addition & 0 deletions .dockerignore
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@@ -0,0 +1 @@
dist/
32 changes: 4 additions & 28 deletions Dockerfile
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Expand Up @@ -31,7 +31,7 @@
FROM ghcr.io/astral-sh/uv:python3.12-alpine AS src
RUN apk add git
COPY . /src
RUN uvx --from build pyproject-build --installer uv -w /src
RUN uv build --wheel /src

#
# Download stages
Expand All @@ -50,12 +50,6 @@
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# FreeSurfer 7.4.1
# FROM downloader AS freesurfer
# COPY docker/files/freesurfer7.4.1-exclude.txt /usr/local/etc/freesurfer7.4.1-exclude.txt
# RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz \
# | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.4.1-exclude.txt

# AFNI
FROM downloader AS afni
# Bump the date to current to update AFNI
Expand All @@ -72,33 +66,16 @@
--exclude "linux_openmp_64/meica.libs" \
# Keep only what we use
&& find /opt/afni-latest -type f -not \( \
-name "3dTshift" -or \
-name "3dUnifize" -or \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete

# PETPVC
FROM downloader AS petpvc
RUN apt-get update && \
apt-get install -y --no-install-recommends ca-certificates curl libinsighttoolkit5.2 && \
rm -rf /var/lib/apt/lists/* && \
curl -fsSL https://github.com/UCL/PETPVC/releases/download/v1.2.10/PETPVC-1.2.10-Linux.tar.gz \
| tar -xz -C /usr/local --strip-components=1 \
PETPVC-1.2.10/bin PETPVC-1.2.10/parc && \
rm -rf /tmp/* /var/tmp/*
-name "3dAutomask" \) \
-delete

# Micromamba
FROM downloader AS micromamba

# Install a C compiler to build extensions when needed.
# traits<6.4 wheels are not available for Python 3.11+, but build easily.
RUN apt-get update && \
apt-get install -y --no-install-recommends build-essential && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

WORKDIR /
# Bump the date to current to force update micromamba
RUN echo "2024.02.06"
RUN echo "2025.08.18"
RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba

ENV MAMBA_ROOT_PREFIX="/opt/conda"
Expand Down Expand Up @@ -175,7 +152,6 @@
# Install files from stages
COPY --from=freesurfer/freesurfer:7.4.1 /usr/local/freesurfer /opt/freesurfer
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=petpvc /usr/local /usr/local

# Simulate SetUpFreeSurfer.sh
ENV OS="Linux" \
Expand All @@ -202,7 +178,7 @@
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users petprep
WORKDIR /home/petprep
ENV HOME="/home/petprep" \

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GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$LD_LIBRARY_PATH'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH:-}"

COPY --from=micromamba /bin/micromamba /bin/micromamba
Expand All @@ -211,7 +187,7 @@
ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate petprep" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/petprep/bin:$PATH" \

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GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$CPATH' (did you mean $PATH?)
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
CPATH="/opt/conda/envs/petprep/include:${CPATH:-}" \
LD_LIBRARY_PATH="/opt/conda/envs/petprep/lib:$LD_LIBRARY_PATH"

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9 changes: 0 additions & 9 deletions REFERENCES.md
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Expand Up @@ -13,27 +13,18 @@
| **FSL** | | https://doi.org/10.1016/j.neuroimage.2004.07.051 https://doi.org/10.1016/j.neuroimage.2008.10.055 https://doi.org/10.1016/j.neuroimage.2011.09.015
| FAST | https://doi.org/10.1109/42.906424 | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST |
| BET | https://doi.org/10.1002/hbm.10062 | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET |
| FLIRT | https://doi.org/10.1006/nimg.2002.1132 https://doi.org/10.1016/S1361-8415(01)00036-6 | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT_BBR |
| MCFLIRT | https://doi.org/10.1006/nimg.2002.1132 | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT |
| SUSAN | https://doi.org/10.1023/A:1007963824710 | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN |
| MELODIC | | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC |
| PRELUDE & FUGUE | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide | https://nipype.readthedocs.io/en/latest/interfaces/generated/workflows.dmri/fsl.utils.html#cleanup-edge-pipeline |
| **AFNI** | | https://doi.org/10.1006/cbmr.1996.0014; https://doi.org/10.1016/j.neuroimage.2011.08.056
| 3dvolreg | | https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html |
| 3dTshift | | https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTshift.html |
| 3dUnifize | | https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dUnifize.html |
| 3dAutomask | | https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAutomask.html |
| **Power, et al. (2012) measures** | https://doi.org/10.1016/j.neuroimage.2011.10.018 | |
| DVARS | https://arxiv.org/abs/1704.01469 https://doi.org/10.1101/125021 | https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#computedvars |
| Framewise displacement | | https://nipype.readthedocs.io/en/latest/interfaces/generated/nipype.algorithms.confounds.html#framewisedisplacement |
| **Other**
| a/tCompCor | https://doi.org/10.1016/j.neuroimage.2007.04.042 | https://nipype.readthedocs.io/en/latest/api/generated/nipype.algorithms.confounds.html#nipype-algorithms-confounds-compcor |
| Connectome Workbench | | https://humanconnectome.org/software/connectome-workbench
| phdiff2fmap | https://doi.org/10.1006/nimg.2001.1054 | https://fmriprep.readthedocs.io/en/stable/sdc/estimation.html#fmriprep.interfaces.fmap.phdiff2fmap |
| nibabel | https://doi.org/10.5281/zenodo.60808 | https://github.com/nipy/nibabel/ |
| nilearn | https://doi.org/10.3389/fninf.2014.00014 | https://github.com/nilearn/nilearn/ |
| nipype | https://doi.org/10.3389/fninf.2011.00013 https://doi.org/10.5281/zenodo.581704 | https://github.com/nipy/nipype/ |
| convert3d | | https://sourceforge.net/projects/c3d/ |
| **Graphics**
| seaborn | https://doi.org/10.5281/zenodo.883859 | https://github.com/mwaskom/seaborn |
| matplotlib 2.0.0 | https://doi.org/10.5281/zenodo.248351 | https://github.com/matplotlib/matplotlib |
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8 changes: 3 additions & 5 deletions env.yml
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Expand Up @@ -29,14 +29,12 @@ dependencies:
- ants=2.6
# Workflow dependencies: Connectome Workbench
- connectome-workbench-cli=2.0
# Workflow dependencies: PETPVC
- petpvc=1.2
# Workflow dependencies: FSL (versions pinned in 6.0.7.17.20250415.fe1c582e)
- fsl-bet2=2111.8
- fsl-flirt=2111.4
- fsl-fast4=2111.3
- fsl-fugue=2201.5
- fsl-mcflirt=2111.0
- fsl-avwutils=2209.3
- fsl-miscmaths=2412.4
- fsl-topup=2203.5
- pip
- pip:
- -r requirements.txt
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