diff --git a/Dockerfile b/Dockerfile index 395c257..1d23b39 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,10 +24,10 @@ FROM pennlinc/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio FROM pennlinc/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba FROM pennlinc/qsiprep-afni:${TAG_AFNI} as build_afni FROM pennlinc/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise -FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda +FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISECUDA} as build_tortoisecuda FROM pennlinc/qsiprep-synb0:${TAG_SYNB0} as build_synb0 FROM pennlinc/atlaspack:0.1.0 as atlaspack -FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 as ubuntu # Make a dummy fsl image containing no FSL FROM ubuntu as no_fsl @@ -58,12 +58,8 @@ ENV ANTSPATH="/opt/ants/bin" \ ANTS_DEPS="zlib1g-dev" ## DSI Studio -ENV QT_BASE_DIR="/opt/qt512" -ENV QTDIR="$QT_BASE_DIR" \ - LD_LIBRARY_PATH="$QT_BASE_DIR/lib/x86_64-linux-gnu:$QT_BASE_DIR/lib:$LD_LIBRARY_PATH" \ - PKG_CONFIG_PATH="$QT_BASE_DIR/lib/pkgconfig:$PKG_CONFIG_PATH" \ - PATH="$QT_BASE_DIR/bin:$PATH:/opt/dsi-studio" \ - DSI_STUDIO_DEPS="qt512base qt512charts-no-lgpl" +ENV PATH="$PATH:/opt/dsi-studio-cpu" \ + DSI_STUDIO_DEPS="qt6-base-dev libqt6charts6-dev" ## MRtrix3 COPY --from=build_mrtrix3 /opt/mrtrix3-latest /opt/mrtrix3-latest @@ -107,7 +103,6 @@ ENV PATH="$PATH:/opt/afni-latest" \ ## TORTOISE COPY --from=build_tortoise /src/TORTOISEV4/bin /src/TORTOISEV4/bin COPY --from=build_tortoise /src/TORTOISEV4/settings /src/TORTOISEV4/settings -COPY --from=build_tortoise /usr/local/boost176 /usr/local/boost176 COPY --from=build_tortoisecuda /src/TORTOISEV4/bin/*cuda /src/TORTOISEV4/bin/ ENV PATH="$PATH:/src/TORTOISEV4/bin" \ TORTOISE_DEPS="fftw3" @@ -140,6 +135,7 @@ RUN apt-get update -qq \ libxm4 \ libxmu6 \ libxt6 \ + libboost-all-dev \ perl \ libtiff5 \ netpbm \ @@ -153,9 +149,6 @@ RUN apt-get update -qq \ && curl -sSL --retry 5 -o /tmp/libxp6.deb https://upenn.box.com/shared/static/reyyundn0l3guvjzghrrv6t4w6md2tjd.deb \ && dpkg -i /tmp/libxp6.deb \ && rm /tmp/libxp6.deb \ - && curl -sSL --retry 5 -o /tmp/libpng.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \ - && dpkg -i /tmp/libpng.deb \ - && rm /tmp/libpng.deb \ && apt-get install -f --no-install-recommends \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* \ @@ -193,13 +186,12 @@ RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/relea dpkg -i pandoc-2.2.2.1-1-amd64.deb && \ rm pandoc-2.2.2.1-1-amd64.deb -# Install qt5.12.8 -RUN add-apt-repository ppa:beineri/opt-qt-5.12.8-bionic \ - && apt-get update \ +# Install qt6 +RUN apt-get update \ && apt install -y --no-install-recommends \ ${DSI_STUDIO_DEPS} ${MRTRIX3_DEPS} ${TORTOISE_DEPS} wget git binutils \ && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -COPY --from=build_dsistudio /opt/dsi-studio /opt/dsi-studio +COPY --from=build_dsistudio /opt/dsi-studio-cpu /opt/dsi-studio-cpu # Install gcc-9 RUN add-apt-repository ppa:ubuntu-toolchain-r/test \ @@ -226,10 +218,6 @@ ENV \ IS_DOCKER_8395080871=1 \ ARTHOME="/opt/art" \ DIPY_HOME=/home/qsiprep/.dipy \ - QTDIR=$QT_BASE_DIR \ - PATH=$QT_BASE_DIR/bin:$PATH \ - LD_LIBRARY_PATH=$QT_BASE_DIR/lib/x86_64-linux-gnu:$QT_BASE_DIR/lib:$LD_LIBRARY_PATH \ - PKG_CONFIG_PATH=$QT_BASE_DIR/lib/pkgconfig:$PKG_CONFIG_PATH \ LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nvidia/cudnn/lib:/opt/freesurfer/lib WORKDIR /root/ @@ -241,8 +229,9 @@ RUN python fetch_templates.py && \ find $HOME/.cache/templateflow -type f -exec chmod go=u {} + # Make it ok for singularity on CentOS -RUN strip --remove-section=.note.ABI-tag /opt/qt512/lib/libQt5Core.so.5.12.8 \ - && ldconfig +RUN for lib in /usr/lib/x86_64-linux-gnu/libQt?Core.so.* ; do \ + strip --remove-section=.note.ABI-tag "$lib" 2>/dev/null || true ; \ + done && ldconfig # Make singularity mount directories RUN mkdir -p /sngl/data \ diff --git a/Dockerfile_3Tissue b/Dockerfile_3Tissue index 77c2ca7..d9370b6 100644 --- a/Dockerfile_3Tissue +++ b/Dockerfile_3Tissue @@ -1,9 +1,9 @@ -FROM nvidia/cuda:11.1.1-devel-ubuntu18.04 +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 ARG TAG_ANTS RUN apt-get update && \ apt-get install -y --no-install-recommends \ - curl git g++ python libeigen3-dev zlib1g-dev libqt5opengl5-dev libqt5svg5-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev libpng-dev unzip + curl git g++ python3 python-is-python3 libeigen3-dev zlib1g-dev libqt6opengl6-dev libqt6svg6-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev libpng-dev unzip ARG MRTRIX_SHA=5f4c31bc93008520c61d59b94af0db3f17b4ab76 ENV PATH="/opt/mrtrix3-latest/bin:$PATH" diff --git a/Dockerfile_AFNI b/Dockerfile_AFNI index a11e11c..98c467c 100644 --- a/Dockerfile_AFNI +++ b/Dockerfile_AFNI @@ -1,4 +1,4 @@ -# Copied from: fMRIPrep Docker Container Image distribution +# Copied and Modified from: fMRIPrep Docker Container Image distribution # # MIT License # @@ -21,12 +21,13 @@ # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. -FROM ubuntu:18.04 +FROM ubuntu:22.04 ARG TAG_ANTS # AFNI latest (neurodocker build) RUN apt-get update -qq \ && apt-get install -y -q --no-install-recommends \ + ca-certificates \ apt-utils \ ed \ gsl-bin \ diff --git a/Dockerfile_ANTs b/Dockerfile_ANTs index 99326c2..2ee4fc7 100644 --- a/Dockerfile_ANTs +++ b/Dockerfile_ANTs @@ -1,4 +1,4 @@ -FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 as base +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 as base ARG TAG_ANTS FROM base as builder @@ -11,7 +11,6 @@ RUN apt-get update && \ gnupg \ software-properties-common \ wget \ - ninja-build \ git \ g++ \ zlib1g-dev \ @@ -24,10 +23,12 @@ RUN apt-get update && \ RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null \ | apt-key add - \ - && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ bionic main' \ + && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ jammy main' \ && apt-get update \ - && apt-get -y install cmake=3.23.2-0kitware1ubuntu18.04.1 cmake-data=3.23.2-0kitware1ubuntu18.04.1 + && apt-get -y install cmake=3.30.2-0kitware1ubuntu22.04.1 \ + cmake-data=3.30.2-0kitware1ubuntu22.04.1 +# Version 2.4.3 : last version using ITK 5.3 ARG ANTS_SHA=caa60eb4ad53d561f9ddd72b71a6baf2acac0078 RUN mkdir /tmp/ants \ && cd /tmp \ @@ -40,8 +41,9 @@ RUN mkdir /tmp/ants \ && mkdir -p /opt/ants \ && git config --global url."https://".insteadOf git:// \ && cmake \ - -GNinja \ - -DBUILD_TESTING=OFF \ + -G "Unix Makefiles" \ + -DBUILD_TESTING:BOOL=OFF \ + -DBUILD_EXAMPLES:BOOL=OFF \ -DCMAKE_C_COMPILER=/usr/bin/gcc-9 \ -DCMAKE_CXX_COMPILER=/usr/bin/g++-9 \ -DBUILD_SHARED_LIBS=ON \ @@ -49,9 +51,9 @@ RUN mkdir /tmp/ants \ -DSuperBuild_ANTS_CXX_OPTIMIZATION_FLAGS="-mtune=x86-64 -march=x86-64" \ -DCMAKE_INSTALL_PREFIX=/opt/ants \ /tmp/ants/source \ - && cmake --build . --parallel 1 \ + && make -j 1 \ && cd ANTS-build \ - && cmake --install . \ + && make install \ && cd /opt/ants/bin \ && rm \ ANTSUseLandmarkImagesToGetAffineTransform \ diff --git a/Dockerfile_DSIStudio b/Dockerfile_DSIStudio index 26264d5..35602a8 100644 --- a/Dockerfile_DSIStudio +++ b/Dockerfile_DSIStudio @@ -1,10 +1,9 @@ -FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 ARG TAG_ANTS -RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub +RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/3bf863cc.pub RUN apt update && apt full-upgrade -y && \ apt install --no-install-recommends -y software-properties-common && \ - add-apt-repository -y ppa:beineri/opt-qt-5.12.8-bionic && \ add-apt-repository -y ppa:ubuntu-toolchain-r/test && \ apt install -y --no-install-recommends \ unzip \ @@ -15,8 +14,8 @@ RUN apt update && apt full-upgrade -y && \ libboost-all-dev \ zlib1g-dev \ ca-certificates \ - qt512base \ - qt512charts-no-lgpl \ + qt6-base-dev \ + libqt6charts6-dev \ mesa-common-dev \ libglu1-mesa-dev \ build-essential \ @@ -31,47 +30,27 @@ RUN apt update && apt full-upgrade -y && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null \ - | apt-key add - \ -&& apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ bionic main' \ -&& apt-get update \ -&& apt-get -y install cmake=3.23.2-0kitware1ubuntu18.04.1 cmake-data=3.23.2-0kitware1ubuntu18.04.1 - + | apt-key add - \ + && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ jammy main' \ + && apt-get update \ + && apt-get -y install cmake=3.30.2-0kitware1ubuntu22.04.1 \ + cmake-data=3.30.2-0kitware1ubuntu22.04.1 #Need to use a different shell so the QT ENV script works SHELL ["/bin/bash", "-c"] -ENV PATH="$PATH:/opt/qt512/bin" -ARG DSI_SHA=03476a67bc96a1d0c90928001b5dd1c490539ee0 -ARG TIPL_SHA=ebd2d8b1ee13d6f87e78db62f2f1a1400b353898 +ARG DSI_DATE=2025.04.16 + +ARG TIPL_SHA=1f89c676df1e3577fe524833d2e67063eebb24f3 -RUN source /opt/qt512/bin/qt512-env.sh \ - && mkdir /opt/dsi-studio \ - && cd /opt/dsi-studio \ - && curl -sSLO https://github.com/frankyeh/DSI-Studio/archive/${DSI_SHA}.zip \ - && unzip ${DSI_SHA}.zip \ - && mv DSI-Studio-${DSI_SHA} src \ - && rm -rf ${DSI_SHA}.zip \ +RUN cd /opt/ \ + && curl -sSLO https://github.com/frankyeh/DSI-Studio/releases/download/${DSI_DATE}/dsi_studio_ubuntu2204_cpu.zip \ + && unzip dsi_studio_ubuntu2204_cpu.zip \ + && rm -rf dsi_studio_ubuntu2204_cpu.zip \ && curl -sSLO https://github.com/frankyeh/TIPL/archive/${TIPL_SHA}.zip \ && unzip ${TIPL_SHA}.zip \ - && mv TIPL-${TIPL_SHA} src/TIPL \ + && mv TIPL-${TIPL_SHA} dsi-studio-cpu/TIPL \ && rm ${TIPL_SHA}.zip \ - && mkdir build && cd build \ - && qmake ../src && make -j 1 + && chmod 755 dsi-studio-cpu/dsi_studio -ARG ATLAS_SHA=bf5afab9b2405f076b1acdf4706c9688525eb713 -ARG UNET_SHA=2e839aae744883983974194dcf6aeff154a82197 +ENV PATH="$PATH:/opt/dsi-studio-cpu" -RUN cd /opt/dsi-studio \ - && mv build/dsi_studio . \ - && chmod 755 dsi_studio \ - && cp -R src/other/* . \ - && rm -rf src build \ - && curl -sSLO https://github.com/frankyeh/UNet-Studio-Data/archive/${UNET_SHA}.zip \ - && unzip ${UNET_SHA}.zip \ - && rm ${UNET_SHA}.zip \ - && mv UNet-Studio-Data-${UNET_SHA}/network/ . \ - && rm -rf mv UNet-Studio-Data-${UNET_SHA} \ - && curl -sSLO https://github.com/frankyeh/DSI-Studio-atlas/archive/${ATLAS_SHA}.zip \ - && unzip ${ATLAS_SHA}.zip \ - && rm -rf DSI-Studio-atlas-${ATLAS_SHA}/.git \ - && mv DSI-Studio-atlas-${ATLAS_SHA} atlas \ - && rm ${ATLAS_SHA}.zip diff --git a/Dockerfile_FSLconda b/Dockerfile_FSLconda index 28698d9..059302a 100644 --- a/Dockerfile_FSLconda +++ b/Dockerfile_FSLconda @@ -1,4 +1,4 @@ -FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 ARG TAG_ANTS RUN apt-get update && \ diff --git a/Dockerfile_FreeSurfer b/Dockerfile_FreeSurfer index ee60ba2..322cf42 100644 --- a/Dockerfile_FreeSurfer +++ b/Dockerfile_FreeSurfer @@ -1,5 +1,5 @@ FROM freesurfer/freesurfer:7.3.1 AS freesurfer -FROM ubuntu:18.04 +FROM ubuntu:22.04 ARG TAG_ANTS COPY --from=freesurfer \ diff --git a/Dockerfile_MRtrix3 b/Dockerfile_MRtrix3 index 1f66c7a..2096e0e 100644 --- a/Dockerfile_MRtrix3 +++ b/Dockerfile_MRtrix3 @@ -1,9 +1,9 @@ -FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 ARG TAG_ANTS RUN apt-get update && \ apt-get install -y --no-install-recommends \ - curl git g++ python libeigen3-dev zlib1g-dev libqt5opengl5-dev libqt5svg5-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev libpng-dev unzip + curl git g++ python3 python-is-python3 libeigen3-dev zlib1g-dev libqt6opengl6-dev libqt6svg6-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev libpng-dev unzip ARG MRTRIX_SHA=670e7b0625572f8b1f13b2793bde506526985d55 ENV PATH="/opt/mrtrix3-latest/bin:$PATH" diff --git a/Dockerfile_Micromamba b/Dockerfile_Micromamba index 16d084f..a93483a 100644 --- a/Dockerfile_Micromamba +++ b/Dockerfile_Micromamba @@ -1,4 +1,4 @@ -# Copied from: fMRIPrep Docker Container Image distribution +# Copied and Modified from: fMRIPrep Docker Container Image distribution # # MIT License # @@ -22,7 +22,7 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. -FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 +FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04 ARG TAG_ANTS RUN apt-get update && \ @@ -55,7 +55,7 @@ COPY qsiprep_env.yml /tmp/env.yml WORKDIR /tmp RUN micromamba config set extract_threads 1 -RUN micromamba create -vv -y -f /tmp/env.yml +RUN micromamba create -c conda-forge -vvv -y -f /tmp/env.yml ENV PATH=/opt/conda/envs/qsiprep/bin:$PATH RUN micromamba clean -y -a diff --git a/Dockerfile_SynB0 b/Dockerfile_SynB0 index 2e712f4..b0673f8 100644 --- a/Dockerfile_SynB0 +++ b/Dockerfile_SynB0 @@ -1,11 +1,11 @@ FROM leonyichencai/synb0-disco:v3.1 AS synb0 -FROM ubuntu:18.04 AS base +FROM ubuntu:22.04 AS base ARG TAG_ANTS FROM alpine AS builder RUN mkdir -p /opt/synb0 \ && cd /opt/synb0 \ - && wget https://raw.githubusercontent.com/MASILab/Synb0-DISCO/master/synb0-license-ccby4.0.txt + && wget https://raw.githubusercontent.com/MASILab/Synb0-DISCO/68f2ba1cae32e2499db585c3eb1b195db4dc2d96/synb0-license-ccby4.0.txt FROM base # Get the SyNb0 models and python executables diff --git a/Dockerfile_TORTOISE b/Dockerfile_TORTOISE index e245ba7..ad2c0f1 100644 --- a/Dockerfile_TORTOISE +++ b/Dockerfile_TORTOISE @@ -2,7 +2,7 @@ ARG TAG_ANTS FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder -RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub +RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/3bf863cc.pub RUN apt update && apt full-upgrade -y && \ apt install --no-install-recommends -y software-properties-common && \ @@ -17,26 +17,17 @@ RUN apt update && apt full-upgrade -y && \ RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null \ | apt-key add - \ - && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ bionic main' \ + && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ jammy main' \ && apt-get update \ - && apt-get -y install cmake=3.23.2-0kitware1ubuntu18.04.1 cmake-data=3.23.2-0kitware1ubuntu18.04.1 + && apt-get -y install cmake=3.30.2-0kitware1ubuntu22.04.1 \ + cmake-data=3.30.2-0kitware1ubuntu22.04.1 +RUN apt install -y libboost-all-dev +ARG TORTOISE_SHA=cea83b5bef845b54c079072f385a087768a60ded RUN \ mkdir /src \ && cd /src \ - && wget https://boostorg.jfrog.io/artifactory/main/release/1.77.0/source/boost_1_77_0.tar.gz \ - && tar -xvf boost_1_77_0.tar.gz \ - && cd boost_1_77_0 \ - && rm /usr/bin/g++ \ - && ln -s /usr/bin/g++-9 /usr/bin/g++ \ - && ./bootstrap.sh --with-libraries=iostreams,filesystem,system,regex --prefix=/usr/local/boost176 \ - && ./b2 install - - -ARG TORTOISE_SHA=5d0c688e85fd12a974d2ecbd8b567913a0b46c4f -RUN \ - cd /src \ && git clone https://github.com/eurotomania/TORTOISEV4.git \ && cd TORTOISEV4/TORTOISEV4 \ && git checkout ${TORTOISE_SHA} \ diff --git a/Dockerfile_TORTOISEcuda b/Dockerfile_TORTOISEcuda index 0d5abc5..d8e2943 100644 --- a/Dockerfile_TORTOISEcuda +++ b/Dockerfile_TORTOISEcuda @@ -2,7 +2,7 @@ ARG TAG_ANTS FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base FROM base as builder -RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub +RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/3bf863cc.pub RUN apt update && apt full-upgrade -y && \ apt install --no-install-recommends -y software-properties-common && \ @@ -17,26 +17,17 @@ RUN apt update && apt full-upgrade -y && \ RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null \ | apt-key add - \ - && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ bionic main' \ + && apt-add-repository -y 'deb https://apt.kitware.com/ubuntu/ jammy main' \ && apt-get update \ - && apt-get -y install cmake=3.23.2-0kitware1ubuntu18.04.1 cmake-data=3.23.2-0kitware1ubuntu18.04.1 + && apt-get -y install cmake=3.30.2-0kitware1ubuntu22.04.1 \ + cmake-data=3.30.2-0kitware1ubuntu22.04.1 +RUN apt install -y libboost-all-dev +ARG TORTOISE_SHA=cea83b5bef845b54c079072f385a087768a60ded RUN \ mkdir /src \ && cd /src \ - && wget https://boostorg.jfrog.io/artifactory/main/release/1.77.0/source/boost_1_77_0.tar.gz \ - && tar -xvf boost_1_77_0.tar.gz \ - && rm /usr/bin/g++ \ - && ln -s /usr/bin/g++-9 /usr/bin/g++ \ - && cd boost_1_77_0 \ - && ./bootstrap.sh --with-libraries=iostreams,filesystem,system,regex --prefix=/usr/local/boost176 \ - && ./b2 install - - -ARG TORTOISE_SHA=5d0c688e85fd12a974d2ecbd8b567913a0b46c4f -RUN \ - cd /src \ && git clone https://github.com/eurotomania/TORTOISEV4.git \ && cd TORTOISEV4/TORTOISEV4 \ && git checkout ${TORTOISE_SHA} \ diff --git a/qsiprep_env.yml b/qsiprep_env.yml index ce862fb..2f02bc9 100755 --- a/qsiprep_env.yml +++ b/qsiprep_env.yml @@ -4,16 +4,18 @@ channels: dependencies: - mkl - mkl-service - - numpy=1.23.5 - - scipy=1.11 - - fury + - numpy==1.26.4 + - scipy==1.11.4 + - vtk==9.3.1 - pip - python=3.10 - pip: - bids-validator==1.14.1 - coverage - - dipy==1.8.0 - - dmri-amico==1.5.4 + - dipy==1.11.0 + - dmri-amico==2.1.0 + - dmri-dicelib==1.2.1 + - fury==0.12.0 - jinja2==3.0.3 - keras==2.8.0 - matplotlib==3.8.3 @@ -21,23 +23,21 @@ dependencies: - nilearn==0.10.1 - nipype==1.8.6 - niworkflows >=1.9,<= 1.10 - - numpy==1.23.5 - pandas==1.5.3 - pillow==10.3.0 - - pyafq==1.3.2 + - pyafq==2.1 - pytest==8.2.2 - pytest-cov==5.0.0 - pytest-env==1.1.3 - protobuf==3.19.6 - - scikit-image==0.22.0 - - scikit-learn==1.4.0 + - scikit-image==0.25.2 + - scikit-learn==1.7.2 - sentry-sdk==1.40.6 - simpleitk==2.3.1 - - spams==2.6.5.4 - sqlalchemy==2.0.27 - templateflow==23.1.0 - tensorflow-gpu==2.8.4 - torch==1.13.1 - transforms3d==0.4.1 - - trx-python==0.2.9 + - trx-python==0.3 - xvfbwrapper==0.2.9 diff --git a/setup_build.sh b/setup_build.sh index ad0a093..ac62865 100644 --- a/setup_build.sh +++ b/setup_build.sh @@ -8,17 +8,17 @@ fi export BUILD_TAG # Versions of the components -export TAG_FSL=24.4.24 -export TAG_FREESURFER=24.9.3 -export TAG_ANTS=24.4.24 -export TAG_MRTRIX3=24.4.24 -export TAG_3TISSUE=24.4.24 -export TAG_DSISTUDIO=24.7.4 -export TAG_MICROMAMBA=24.7.1 -export TAG_AFNI=23.3.2 -export TAG_TORTOISE=24.4.29 -export TAG_TORTOISECUDA=24.4.29 -export TAG_SYNB0=24.9.0 +export TAG_FSL=25.11.14 +export TAG_FREESURFER=25.11.14 +export TAG_ANTS=25.11.14 +export TAG_MRTRIX3=25.11.14 +export TAG_3TISSUE=25.11.14 +export TAG_DSISTUDIO=25.11.14 +export TAG_MICROMAMBA=25.11.14 +export TAG_AFNI=25.11.14 +export TAG_TORTOISE=25.11.14 +export TAG_TORTOISECUDA=25.11.14 +export TAG_SYNB0=25.11.14 echo "Settings:" echo "----------"