Merge branch 'master' into 'dev'

.github/workflows/checks.yml

@@ -29,7 +29,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
+         sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy libpng-dev
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]
@@ -90,7 +90,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
+         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy libpng-dev
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]

.github/workflows/releases.yml

@@ -0,0 +1,137 @@
+name: Releases
+
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: 'Branch to release from'
+        required: true
+        default: 'dev'
+
+jobs:
+  linux-release:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.inputs.branch }}
+
+      - name: Set env vars
+        id: envs
+        run: |
+          commit_sha=$(git rev-parse HEAD)
+          date=$(date +%Y_%m_%d)
+          echo "commit_sha=$commit_sha" >> $GITHUB_OUTPUT
+          echo "date=$date" >> $GITHUB_OUTPUT
+          echo "output_name=mrtrix3-linux-$commit_sha-$date" >> $GITHUB_OUTPUT
+
+      - name: Install Eigen3
+        run: |
+          git clone https://gitlab.com/libeigen/eigen.git && cd eigen && git checkout 3.4.0
+          cmake -B build && cmake --build build
+          sudo cmake --install build
+
+      - name: Install Qt 6
+        uses: jurplel/install-qt-action@v3
+        with:
+          version: '6.7.0'
+          set-env: true
+
+      - name: Run build
+        run: |
+          ./packaging/package-linux-tarball.sh .
+          mv mrtrix.tar.gz ${{ steps.envs.outputs.output_name }}.tar.gz
+
+      - name: Upload release artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ steps.envs.outputs.output_name }}
+          path: ${{ steps.envs.outputs.output_name }}.tar.gz
+
+  macos-release:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.inputs.branch }}
+
+      - name: Set env vars
+        id: envs
+        run: |
+          commit_sha=$(git rev-parse HEAD)
+          date=$(date +%Y_%m_%d)
+          echo "commit_sha=$commit_sha" >> $GITHUB_OUTPUT
+          echo "date=$date" >> $GITHUB_OUTPUT
+          echo "output_name=mrtrix3-macos-$commit_sha-$date" >> $GITHUB_OUTPUT
+
+      - name: Install deps
+        run: brew install numpy cmake qt eigen pkg-config fftw libpng ninja
+
+      - name: Run build
+        run: |
+          cd ./packaging/macos
+          ./build ${{ github.event.inputs.branch }}
+          mv ./mrtrix3-macos-${{ github.event.inputs.branch }}.tar.xz ../../${{ steps.envs.outputs.output_name }}.tar.xz
+
+      - name: Upload release artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ steps.envs.outputs.output_name }}
+          path: ${{ steps.envs.outputs.output_name }}.tar.xz
+
+  windows-release:
+    runs-on: windows-latest
+    defaults:
+      run:
+        shell: msys2 {0}
+
+    env:
+      MINGW_PACKAGE_PREFIX: mingw-w64-ucrt-x86_64
+
+    steps:
+      - uses: msys2/setup-msys2@v2
+        with:
+          msystem: UCRT64
+          install: |
+            git
+            python
+            ${{env.MINGW_PACKAGE_PREFIX}}-bc
+            ${{env.MINGW_PACKAGE_PREFIX}}-cmake
+            ${{env.MINGW_PACKAGE_PREFIX}}-diffutils
+            ${{env.MINGW_PACKAGE_PREFIX}}-eigen3
+            ${{env.MINGW_PACKAGE_PREFIX}}-fftw
+            ${{env.MINGW_PACKAGE_PREFIX}}-gcc
+            ${{env.MINGW_PACKAGE_PREFIX}}-libtiff
+            ${{env.MINGW_PACKAGE_PREFIX}}-ninja
+            ${{env.MINGW_PACKAGE_PREFIX}}-pkg-config
+            ${{env.MINGW_PACKAGE_PREFIX}}-qt6-base
+            ${{env.MINGW_PACKAGE_PREFIX}}-qt6-svg
+            ${{env.MINGW_PACKAGE_PREFIX}}-zlib
+
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.inputs.branch }}
+
+      - name: Set env vars
+        id: envs
+        run: |
+          commit_sha=$(git rev-parse HEAD)
+          date=$(date +%Y_%m_%d)
+          echo "commit_sha=$commit_sha" >> $GITHUB_OUTPUT
+          echo "date=$date" >> $GITHUB_OUTPUT
+          echo "output_name=mrtrix3-windows-$commit_sha-$date" >> $GITHUB_OUTPUT
+
+      - name: Run build
+        run: |
+          cd packaging/mingw
+          ./run.sh ${{ steps.envs.outputs.commit_sha }} mrtrix3
+          mv mingw*.tar.zst ../../../${{ steps.envs.outputs.output_name }}.tar.zst
+
+      - name: Upload release artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ steps.envs.outputs.output_name }}
+          path: ${{ steps.envs.outputs.output_name }}.tar.zst

.github/workflows/weekly_sanitizers.yml

@@ -0,0 +1,62 @@
+name: Sanitizers checks
+
+on:
+  workflow_dispatch:
+  # Run this every Sunday at midnight
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  linux-clang-build:
+    runs-on: ubuntu-latest
+
+    env:
+      SCCACHE_GHA_ENABLED: "true"
+      SCCACHE_CACHE_SIZE: "2G"
+
+    strategy:
+        fail-fast: false
+        matrix:
+            sanitizer: [address, thread, undefined]
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        submodules: true
+        ref: dev
+
+    - name: install dependencies
+      run: |
+         sudo apt-get update
+         sudo apt-get install clang llvm qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
+
+    - name: Run sccache-cache
+      uses: mozilla-actions/[email protected]
+
+    - name: Get CMake
+      uses: lukka/get-cmake@latest
+      with:
+        cmakeVersion: '3.16.3'
+
+    - name: Print CMake version
+      run: cmake --version
+
+    - name: configure
+      run: >
+        cmake
+        -B build
+        -G Ninja
+        -D CMAKE_BUILD_TYPE=RelWithDebInfo
+        -D MRTRIX_BUILD_TESTS=ON
+        -D ECM_ENABLE_SANITIZERS=${{ matrix.sanitizer }}
+        -D CMAKE_C_COMPILER=clang
+        -D CMAKE_CXX_COMPILER=clang++
+
+    - name: build
+      run: cmake --build build
+
+    - name: binary tests
+      run: cd build && ctest -L binary --output-on-failure
+
+    - name: unit tests
+      run: cd build && ctest -L unittest --output-on-failure

Dockerfile

@@ -2,7 +2,7 @@ ARG MAKE_JOBS="1"
 ARG DEBIAN_FRONTEND="noninteractive"
 
 FROM python:3.8-slim AS base
-FROM buildpack-deps:buster AS base-builder
+FROM buildpack-deps:bookworm AS base-builder
 
 FROM base-builder AS mrtrix3-builder
 
@@ -21,39 +21,42 @@ RUN apt-get -qq update \
         libpng-dev \
         libqt5opengl5-dev \
         libqt5svg5-dev \
-        qt5-default \
+        libtiff5-dev \
+        qtbase5-dev \
         zlib1g-dev \
     && rm -rf /var/lib/apt/lists/*
 
 # Clone, build, and install MRtrix3.
 ARG MAKE_JOBS
 WORKDIR /opt/mrtrix3
 RUN git clone -b $MRTRIX3_GIT_COMMITISH --depth 1 https://github.com/MRtrix3/mrtrix3.git . \
-    && ./configure $MRTRIX3_CONFIGURE_FLAGS \
-    && NUMBER_OF_PROCESSORS=$MAKE_JOBS ./build $MRTRIX3_BUILD_FLAGS \
+    && python3 ./configure $MRTRIX3_CONFIGURE_FLAGS \
+    && NUMBER_OF_PROCESSORS=$MAKE_JOBS python3 ./build $MRTRIX3_BUILD_FLAGS \
     && rm -rf tmp
 
 # Download minified ART ACPCdetect (V2.0).
-FROM base-builder as acpcdetect-installer
+FROM base-builder AS acpcdetect-installer
 WORKDIR /opt/art
 RUN curl -fsSL https://osf.io/73h5s/download \
     | tar xz --strip-components 1
 
 # Download minified ANTs (2.3.4-2).
-FROM base-builder as ants-installer
+FROM base-builder AS ants-installer
 WORKDIR /opt/ants
 RUN curl -fsSL https://osf.io/yswa4/download \
     | tar xz --strip-components 1
 
 # Download FreeSurfer files.
-FROM base-builder as freesurfer-installer
+FROM base-builder AS freesurfer-installer
 WORKDIR /opt/freesurfer
 RUN curl -fsSLO https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
 
-# Download minified FSL (6.0.4-2)
-FROM base-builder as fsl-installer
+# Download minified FSL (6.0.7.7)
+# TODO May be separate evolution of this dependency that needs to be addressed
+#   (or do #2684 / #2601)
+FROM base-builder AS fsl-installer
 WORKDIR /opt/fsl
-RUN curl -fsSL https://osf.io/dtep4/download \
+RUN curl -fsSL https://osf.io/ph9ex/download \
     | tar xz --strip-components 1
 
 # Build final image.
@@ -65,7 +68,8 @@ RUN apt-get -qq update \
         binutils \
         dc \
         less \
-        libfftw3-3 \
+        libfftw3-single3 \
+        libfftw3-double3 \
         libgl1-mesa-glx \
         libgomp1 \
         liblapack3 \
@@ -76,7 +80,9 @@ RUN apt-get -qq update \
         libqt5svg5 \
         libqt5widgets5 \
         libquadmath0 \
+        libtiff5-dev \
         python3-distutils \
+        procps \
     && rm -rf /var/lib/apt/lists/*
 
 COPY --from=acpcdetect-installer /opt/art /opt/art
@@ -93,12 +99,13 @@ ENV ANTSPATH="/opt/ants/bin" \
     FSLMULTIFILEQUIT="TRUE" \
     FSLTCLSH="/opt/fsl/bin/fsltclsh" \
     FSLWISH="/opt/fsl/bin/fslwish" \
-    LD_LIBRARY_PATH="/opt/fsl/lib:$LD_LIBRARY_PATH" \
-    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
+    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"
 
 # Fix "Singularity container cannot load libQt5Core.so.5" on CentOS 7
 RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 \
     && ldconfig \
     && apt-get purge -yq binutils
 
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
 CMD ["/bin/bash"]

Singularity

@@ -26,8 +26,8 @@ Include: apt
     export FSLDIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH
 
 # All
-    LD_LIBRARY_PATH="/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH"
-    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
+    LD_LIBRARY_PATH="/.singularity.d/libs:/usr/lib:$LD_LIBRARY_PATH"
+    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"
     export LD_LIBRARY_PATH PATH
 
 %post
@@ -51,8 +51,10 @@ Include: apt
     mkdir -p /opt/ants && curl -fsSL https://osf.io/yswa4/download | tar xz -C /opt/ants --strip-components 1
     # Download FreeSurfer lookup table file (v7.1.1).
     mkdir -p /opt/freesurfer && curl -fsSL -o /opt/freesurfer/FreeSurferColorLUT.txt https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
-    # Download minified FSL (6.0.4-2).
-    mkdir -p /opt/fsl && curl -fsSL https://osf.io/dtep4/download | tar xz -C /opt/fsl --strip-components 1
+    # Download minified FSL (6.0.7.7).
+    # TODO May be separate evolutions of this dependency that require merging
+    #   (or obviate through #2684 / #2601)
+    mkdir -p /opt/fsl && curl -fsSL https://osf.io/ph9ex/download | tar xz -C /opt/fsl --strip-components 1
 
 # Use Python3 for anything requesting Python, since Python2 is not installed
     ln -s /usr/bin/python3 /usr/bin/python

check_syntax

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

clang-format-all

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright (c) 2008-2024 the MRtrix3 contributors.
+# Copyright (c) 2008-2025 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

cpp/cmd/5tt2gmwmi.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cpp/cmd/5tt2vis.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cpp/cmd/5ttcheck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -146,10 +146,11 @@ void run() {
   }
 
   const std::string vox_option_suggestion =
-      get_options("masks").empty()
-          ? " (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)"
+      get_options("voxels").empty()
+          ? " (suggest re-running using the -voxels option "
+            "to see voxels where tissue fractions do not sum to 1.0)"
           : (" (suggest checking " + std::string(argument.size() > 1 ? "outputs from" : "output of") +
-             " -masks option)");
+             " -voxels option)");
 
   if (major_error_count) {
     if (argument.size() > 1)

cpp/cmd/5ttedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+/* Copyright (c) 2008-2025 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this