[WIP] Update Ubuntu base and Cuda

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 \

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"

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 \

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 \
@@ -40,18 +41,19 @@ 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 \
         -DSuperBuild_ANTS_C_OPTIMIZATION_FLAGS="-mtune=x86-64 -march=x86-64" \
         -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 \

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

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 && \

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 \

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"

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
 

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

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} \