diff --git a/recipes/mrtrix3src/README.md b/recipes/mrtrix3src/README.md new file mode 100644 index 00000000..56652d30 --- /dev/null +++ b/recipes/mrtrix3src/README.md @@ -0,0 +1,22 @@ + +---------------------------------- +## mrtrix3src/toolVersion ## +MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. This is the current version, built from source (not a release). + + +Example: +``` +mrview +``` + +More documentation can be found here: https://mrtrix.readthedocs.io/en/toolVersion/ + +Citation: +``` +J.-D. Tournier, R. E. Smith, D. Raffelt, R. Tabbara, T. Dhollander, M. Pietsch, D. Christiaens, B. Jeurissen, C.-H. Yeh, and A. Connelly. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 202 (2019), pp. 116–37. +``` + + +To run container outside of this environment: ml mrtrix3src/toolVersion + +---------------------------------- diff --git a/recipes/mrtrix3src/build.sh b/recipes/mrtrix3src/build.sh new file mode 100755 index 00000000..4a66ab99 --- /dev/null +++ b/recipes/mrtrix3src/build.sh @@ -0,0 +1,41 @@ +#!/usr/bin/env bash +set -e + +export toolName='mrtrix3src' +export toolVersion='latest' +# Don't forget to update version change in README.md!!!!! +# https://github.com/MRtrix3/mrtrix3/releases/ + +if [ "$1" != "" ]; then + echo "Entering Debug mode" + export debug=$1 +fi + +source ../main_setup.sh + +neurodocker generate ${neurodocker_buildMode} \ + --base-image vnmd/fsl_6.0.5.1:20221016 \ + --pkg-manager apt \ + --ants version="2.3.4" \ + --workdir /opt \ + --install dbus-x11 less python3-distutils mesa-common-dev libglu1-mesa qt5-default libqt5svg5-dev wget libqt5opengl5-dev libqt5opengl5 libqt5gui5 libqt5core5a libtiff5-dev libtiff5 libfftw3-dev liblapack3 libeigen3-dev \ + --run="wget https://github.com/MRtrix3/mrtrix3/archive/refs/heads/master.zip \ + && unzip ./master.zip && mv mrtrix3-master mrtrix3-${toolVersion} && rm master.zip" \ + --workdir /opt/mrtrix3-${toolVersion} \ + --run "python3 configure" \ + --run "python3 build" \ + --run "ln -s /usr/bin/python3 /usr/bin/python" \ + --workdir /opt/acpcdetect_V2.1 \ + --run="wget https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/build/acpcdetect_V2.1_LinuxCentOS6.7.tar.gz \ + && tar zxvf acpcdetect_V2.1_LinuxCentOS6.7.tar.gz \ + && rm -rf acpcdetect_V2.1_LinuxCentOS6.7.tar.gz" \ + --env ARTHOME=/opt/acpcdetect_V2.1/ \ + --env PATH='$PATH':/opt/mrtrix3-${toolVersion}/bin:/opt/acpcdetect_V2.1/bin \ + --env DEPLOY_PATH=/opt/mrtrix3-${toolVersion}/bin/:/opt/acpcdetect_V2.1/bin \ + --copy README.md /README.md \ + --user=neuro \ + > ${imageName}.${neurodocker_buildExt} + +if [ "$1" != "" ]; then + ./../main_build.sh +fi diff --git a/recipes/mrtrix3src/test.sh b/recipes/mrtrix3src/test.sh new file mode 100644 index 00000000..fb730815 --- /dev/null +++ b/recipes/mrtrix3src/test.sh @@ -0,0 +1,5 @@ +dwifslpreproc +# shouldn't through any errors (e.g. distutils, no python available ...) + +mrview +# should open up ok -> needs QT and doesn't come from neurodocker -> we tried a pull request, but it didn't get merged. \ No newline at end of file