Merge tag '3.0.4' into merge-with-main-mrtrix

tagged version 3.0.4

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,48 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[command]: [bug report title]"
+labels: bug
+assignees: ''
+
+---
+
+Please use this form for *bug reports only*; for installation problems, and general questions and support, please consult the [community forum](http://community.mrtrix.org/search?expanded=true).
+
+**Describe the bug**
+
+A clear and concise description of what the bug is; including if appropriate
+how the observed behaviour differs from that expected.
+
+**To Reproduce**
+
+Steps to reproduce the behaviour.
+
+If the issue is data-dependent, please consider providing a link to
+(anonymised) data to assist developers in reproducing the bug.
+
+**Platform/Environment/Version**
+
+Please provide the following information:
+
+-  OS: (ubuntu: `lsb_release -a`, macOS: `sw_vers -productVersion`) [e.g. Ubuntu 16.04]
+
+-  *MRtrix3* version (example: `mrinfo -version`) [ e.g. `3.0_RC3-309-g0074bc6c` ]
+
+---
+
+**Advanced debugging information (if applicable)**
+
+-  In case of a critical error such as "segmentation fault", please generate
+   and report the backtrace as described [here](https://community.mrtrix.org/t/advanced-debugging-of-mrtrix3-binaries).
+
+- For issues with `mrview`, please provide:
+
+   -  Information about the Qt version; one of the following:
+
+      -  `grep "Qt:" $(dirname $(which mrview))/../config`
+
+      -  Open `mrview` --> `[i]` --> About Qt
+
+   -  In the case of crashes or rendering issues, the information from:
+      `mrview -exit -debug`.

.github/workflows/checks.yml

@@ -9,6 +9,7 @@ on:
 
 
 
+
 jobs:
   linux-clang-build:
 
@@ -24,7 +25,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang-8 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
+         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
 
     - name: configure
       run: ./configure -assert || { cat configure.log; false; }
@@ -161,7 +162,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install pylint3 python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme python3-pip
+         sudo apt-get install pylint python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme python3-pip
          pip3 install sphinx-notfound-page
 
 
@@ -180,7 +181,7 @@ jobs:
       run: python3 -m sphinx -n -N -W -w sphinx.log docs/ tmp/
 
     - name: install build dependencies
-      run: sudo apt-get install clang-8 libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
+      run: sudo apt-get install python2 clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
 
     - name: check configure with Python 2
       run: python2 ./configure || { cat configure.log; false; }

Dockerfile

@@ -7,7 +7,7 @@ FROM buildpack-deps:buster AS base-builder
 FROM base-builder AS mrtrix3-builder
 
 # Git commitish from which to build MRtrix3.
-ARG MRTRIX3_GIT_COMMITISH="3.0.3"
+ARG MRTRIX3_GIT_COMMITISH="3.0.4"
 # Command-line arguments for `./configure`
 ARG MRTRIX3_CONFIGURE_FLAGS=""
 # Command-line arguments for `./build`
@@ -40,21 +40,21 @@ WORKDIR /opt/art
 RUN curl -fsSL https://osf.io/73h5s/download \
     | tar xz --strip-components 1
 
-# Download minified ANTs (2.3.4).
+# Download minified ANTs (2.3.4-2).
 FROM base-builder as ants-installer
 WORKDIR /opt/ants
-RUN curl -fsSL https://osf.io/3ad69/download \
+RUN curl -fsSL https://osf.io/yswa4/download \
     | tar xz --strip-components 1
 
 # Download FreeSurfer files.
 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)
+# Download minified FSL (6.0.4-2)
 FROM base-builder as fsl-installer
 WORKDIR /opt/fsl
-RUN curl -fsSL https://osf.io/dv258/download \
+RUN curl -fsSL https://osf.io/dtep4/download \
     | tar xz --strip-components 1
 
 # Build final image.
@@ -63,6 +63,7 @@ FROM base AS final
 # Install runtime system dependencies.
 RUN apt-get -qq update \
     && apt-get install -yq --no-install-recommends \
+        binutils \
         dc \
         less \
         libfftw3-3 \
@@ -73,6 +74,7 @@ RUN apt-get -qq update \
         libqt5core5a \
         libqt5gui5 \
         libqt5network5 \
+        libqt5svg5 \
         libqt5widgets5 \
         libquadmath0 \
         libtiff5 \
@@ -96,5 +98,9 @@ ENV ANTSPATH="/opt/ants/bin" \
     LD_LIBRARY_PATH="/opt/fsl/lib:$LD_LIBRARY_PATH" \
     PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
 
-WORKDIR /work
+# 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
+
 CMD ["/bin/bash"]

Singularity

@@ -24,10 +24,10 @@ Include: apt
     FSLTCLSH=/opt/fsl/bin/fsltclsh
     FSLWISH=/opt/fsl/bin/fslwish
     export FSLDIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH
-    
+
 # All
-    LD_LIBRARY_PATH="/usr/local/cuda/lib64:/usr/local/cuda/bin:/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH"
-    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:/usr/local/cuda/bin:$PATH"
+    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"
     export LD_LIBRARY_PATH PATH
 
 %post
@@ -39,30 +39,33 @@ Include: apt
     apt-get update && apt-get upgrade -y
 
 # Runtime requirements
-    apt-get update && apt-get install -y --no-install-recommends dc less libfftw3-bin liblapack3 libpng16-16 libqt5network5 libqt5widgets5 libtiff5 python3 python3-distutils zlib1g
+    apt-get update && apt-get install -y --no-install-recommends dbus dc less libfftw3-bin liblapack3 libpng16-16 libqt5network5 libqt5widgets5 libtiff5 python3 python3-distutils zlib1g
 
 # Build requirements
     apt-get update && apt-get install -y --no-install-recommends build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev
 
 # Neuroimaging software / data dependencies
     # Download minified ART ACPCdetect (V2.0).
     mkdir -p /opt/art && curl -fsSL https://osf.io/73h5s/download | tar xz -C /opt/art --strip-components 1
-    # Download minified ANTs (2.3.4).
-    mkdir -p /opt/ants && curl -fsSL https://osf.io/3ad69/download | tar xz -C /opt/ants --strip-components 1
+    # Download minified ANTs (2.3.4-2).
+    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).
-    mkdir -p /opt/fsl && curl -fsSL https://osf.io/dv258/download | tar xz -C /opt/fsl --strip-components 1
+    # 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
 
 # Use Python3 for anything requesting Python, since Python2 is not installed
     ln -s /usr/bin/python3 /usr/bin/python
 
 # MRtrix3 setup
-    git clone -b 3.0.3 --depth 1 https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3
+    git clone -b 3.0.4 --depth 1 https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3
     cd /opt/mrtrix3 && ./configure && ./build -persistent -nopaginate && rm -rf testing/ tmp/ && cd ../../
 
 # apt cleanup to recover as much space as possible
-    apt-get remove -y build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+    apt-get remove -y build-essential ca-certificates curl git libeigen3-dev libfftw3-dev libgl1-mesa-dev libpng-dev libqt5opengl5-dev libqt5svg5-dev libtiff5-dev qt5-qmake qtbase5-dev-tools wget zlib1g-dev && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Configure DBus to facilitate mrview execution
+    dbus-uuidgen
 
 %runscript
-    exec /usr/bin/bash -c "$@"
+    exec "$@"

bin/5ttgen

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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

bin/blend

@@ -1,6 +1,6 @@
 #!/usr/bin/env python2
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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
@@ -15,6 +15,9 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
+# note: deal with these warnings properly when we drop support for Python 2:
+# pylint: disable=consider-using-f-string
+
 import os
 import sys
 

bin/convert_bruker

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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
@@ -15,6 +15,9 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
+# note: deal with these warnings properly when we drop support for Python 2:
+# pylint: disable=unspecified-encoding
+
 import sys, os.path
 
 if len (sys.argv) != 3:

bin/dwi2response

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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
@@ -100,19 +100,20 @@ def execute(): #pylint: disable=unused-variable
 
   app.goto_scratch_dir()
 
-  if app.ARGS.mask:
-    # Check that the brain mask is appropriate
-    mask_header = image.Header('mask.mif')
-    if mask_header.size()[:3] != image.Header('dwi.mif').size()[:3]:
-      raise MRtrixError('Dimensions of provided mask image do not match DWI')
-    if not (len(mask_header.size()) == 3 or (len(mask_header.size()) == 4 and mask_header.size()[3] == 1)):
-      raise MRtrixError('Provided mask image needs to be a 3D image')
-  else:
-    app.console('Computing brain mask (dwi2mask)...')
-    run.command('dwi2mask dwi.mif mask.mif', show=False)
-
-  if not image.statistics('mask.mif', mask='mask.mif').count:
-    raise MRtrixError(('Provided' if app.ARGS.mask else 'Generated') + ' mask image does not contain any voxels')
+  if alg.supports_mask():
+    if app.ARGS.mask:
+      # Check that the brain mask is appropriate
+      mask_header = image.Header('mask.mif')
+      if mask_header.size()[:3] != image.Header('dwi.mif').size()[:3]:
+        raise MRtrixError('Dimensions of provided mask image do not match DWI')
+      if not (len(mask_header.size()) == 3 or (len(mask_header.size()) == 4 and mask_header.size()[3] == 1)):
+        raise MRtrixError('Provided mask image needs to be a 3D image')
+    else:
+      app.console('Computing brain mask (dwi2mask)...')
+      run.command('dwi2mask dwi.mif mask.mif', show=False)
+
+    if not image.statistics('mask.mif', mask='mask.mif').count:
+      raise MRtrixError(('Provided' if app.ARGS.mask else 'Generated') + ' mask image does not contain any voxels')
 
   # From here, the script splits depending on what estimation algorithm is being used
   alg.execute()

bin/dwibiascorrect

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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

bin/dwicat

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (c) 2008-2021 the MRtrix3 contributors.
+# Copyright (c) 2008-2022 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
@@ -15,9 +15,12 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
+# note: deal with these warnings properly when we drop support for Python 2:
+# pylint: disable=unspecified-encoding
 
 
-import json
+
+import json, shutil
 
 
 
@@ -36,7 +39,7 @@ def usage(cmdline): #pylint: disable=unused-variable
 
 
 def execute(): #pylint: disable=unused-variable
-  from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
+  from mrtrix3 import CONFIG, MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
   from mrtrix3 import app, image, path, run #pylint: disable=no-name-in-module, import-outside-toplevel
 
   num_inputs = len(app.ARGS.inputs)
@@ -45,13 +48,26 @@ def execute(): #pylint: disable=unused-variable
 
   # check input data
   def check_header(header):
-    if len(header.size()) != 4:
-      raise MRtrixError('Image "' + header.name() + '" is not a 4D image series')
+    if len(header.size()) > 4:
+      raise MRtrixError('Image "' + header.name() + '" contains more than 4 dimensions')
     if not 'dw_scheme' in header.keyval():
       raise MRtrixError('Image "' + header.name() + '" does not contain a gradient table')
-    num_grad_lines = len(header.keyval()['dw_scheme'])
-    if num_grad_lines != header.size()[3]:
-      raise MRtrixError('Number of lines in gradient table for image "' + header.name() + '" (' + str(num_grad_lines) + ') does not match number of volumes (' + str(header.size()[3]) + ')')
+    dw_scheme = header.keyval()['dw_scheme']
+    try:
+      if isinstance(dw_scheme[0], list):
+        num_grad_lines = len(dw_scheme)
+      elif (isinstance(dw_scheme[0], ( int, float))) and len(dw_scheme) >= 4:
+        num_grad_lines = 1
+      else:
+        raise MRtrixError
+    except (IndexError, MRtrixError):
+      raise MRtrixError('Image "' + header.name() + '" contains gradient table of unknown format')
+    if len(header.size()) == 4:
+      num_volumes = header.size()[3]
+      if num_grad_lines != num_volumes:
+        raise MRtrixError('Number of lines in gradient table for image "' + header.name() + '" (' + str(num_grad_lines) + ') does not match number of volumes (' + str(num_volumes) + ')')
+    elif not (num_grad_lines == 1 and len(dw_scheme) >= 4 and dw_scheme[3] <= float(CONFIG.get('BZeroThreshold', 10.0))):
+      raise MRtrixError('Image "' + header.name() + '" is 3D, and cannot be validated as a b=0 volume')
 
   first_header = image.Header(path.from_user(app.ARGS.inputs[0], False))
   check_header(first_header)
@@ -87,7 +103,12 @@ def execute(): #pylint: disable=unused-variable
 
   # extract b=0 volumes within each input series
   for index in range(0, num_inputs):
-    run.command('dwiextract ' + str(index) + 'in.mif ' + str(index) + 'b0.mif -bzero')
+    infile = str(index) + 'in.mif'
+    outfile = str(index) + 'b0.mif'
+    if len(image.Header(infile).size()) > 3:
+      run.command('dwiextract ' + infile + ' ' + outfile + ' -bzero')
+    else:
+      run.function(shutil.copyfile, infile, outfile)
 
   mask_option = ' -mask_input mask.mif -mask_target mask.mif' if app.ARGS.mask else ''