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davidmeunier79davidmeunier79
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Correct petra stevie gcc 0.25 instead of 5 + robust for marmo + added copy of macapype Dockerfile to avoid an space issues on github actsions servers(#54)
* petra_erode/dilate gcc 0.25 instead of 5 + robust for marmo + added copy of macapype Dockerfile to avoid an space issues on github actsions servers
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‎Dockerfile‎

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#
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# Timestamp: 2020/12/02 18:33:44 UTC
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FROM macatools/macapype:latest
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FROM macatools/macapype_env:v0.3.2
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USER root
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ARG DEBIAN_FRONTEND="noninteractive"
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MAINTAINER David Meunier "david.meunier@univ-amu.fr"
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######################## Python packages
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RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
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RUN python -m pip install xvfbwrapper \
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psutil \
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numpy \
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scipy \
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matplotlib \
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statsmodels \
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pandas \
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networkx\
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mock \
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prov \
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click \
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funcsigs \
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pydotplus \
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pydot \
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rdflib \
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pbr \
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nibabel \
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packaging \
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pytest
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RUN python -m pip install graphviz \
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pybids \
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nipype \
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nilearn \
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scikit-image \
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brain-slam
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RUN python -m pip install SimpleITK
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############################################# install macapype
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RUN python -m pip install --pre macapype
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RUN python -c "import macapype; print(macapype.__version__)"
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############################################# install skullTo3d
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RUN python -m pip install --no-deps --pre skullTo3d
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RUN python -c "import skullTo3d; print(skullTo3d.__version__)"
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################################################## Finishing
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RUN apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN rm -rf \
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/tmp/hsperfdata* \
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/var/*/apt/*/partial \
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/var/log/apt/term*

‎workflows/params_segment_macaque_ants_4animal_skullnoisypetra.json‎

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"petra_head_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_dilate":
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"petra_skull_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_fov":
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{
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"brainsize": 45

‎workflows/params_segment_macaque_ants_quick_skullnoisypetra.json‎

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"petra_head_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_dilate":
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"petra_skull_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_fov":
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{
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"brainsize": 45

‎workflows/params_segment_macaque_ants_skullnoisypetra.json‎

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"petra_head_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 3.0
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},
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"petra_head_dilate":
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"petra_skull_gcc_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_gcc_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 5.0
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"kernel_size": 1.0
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},
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"petra_skull_dilate":
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{
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"operation": "modal",
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_erode":
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{
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"kernel_shape": "boxv",
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"kernel_size": 7.0
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"kernel_size": 3.0
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},
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"petra_skull_fov":
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{
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"brainsize": 45

‎workflows/params_segment_marmo_ants_4animal_skull.json‎

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"bet4animal":
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{
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"label": 3,
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"f": 0.3,
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"robust": false
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"f": 0.25,
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"robust": true
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}
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},
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"debias":

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