Installing MANTiS

MANTiS is provided as a combination of matlab and c++ code. It needs to be built for your platform. So far we have only tested on Linux systems. In principle it should also work on OSX if SPM works.

Prerequisites

The build process requires the following tools:

1. git
2. cmake
3. c++ compiler

Decisions to make

MANTiS eventually needs to reside in the spm/toolbox folder. You can carry out the commands below in that folder or perform them elsewhere and copy the results to spm/toolbox. The advantage of doing everything in the spm/toolbox is that it is easier to update the installation.

Downloading

The source code must be fetched using git, and there are several steps. Type the following into a terminal. These commands fetch the MANTiS code, plus some dependencies.

git clone https://github.com/DevelopmentalImagingMCRI/mantis.git
cd mantis
git submodule init
git submodule update

Updates to mantis can be fetched using

git pull

Updates to c++ parts will require a rebuild to take effect.

Developers

MANTiS is hosted on github

Build ITK components

The following commands use the SuperBuild process, that fetches a specific ITK version and builds it. This takes a while. If you know what you are doing you may be able to use a system version of ITK. Make sure you match up the installation directory with the SuperBuild version

The build process requires cmake and git and a compiler.

cd ITKStuff

On linux/mac:

## Make a build directory with the matlab architecture in the name

export ARCH=$(echo "disp(sprintf('\n%s', computer)),quit" | matlab -nojvm -nodesktop -nosplash |tail -1)

mkdir Build.${ARCH} 

Finally, trigger a build:

cd Build.${ARCH}

cmake ../SuperBuild
## increase if you have lots of cores
make -j2

executables named segCSF , cleanWM and neonateScalper will be in

mantis/ITKStuff/Build.${ARCH}/MANTiS-build/bin/

You can delete build files to save space:

rm -rf ITK-build ITK-prefix ITK

Preliminary windows instructions

We have only performed limited testing, with 64 bit Windows and the MSYS2 compiler suite. Substituting 32 bit alternatives may work for 32 bit windows, provided you change the directory name, as discussed below.

Install MSYS 64 bit

Fetch and run the 64 bit msys installer

Update the base system from the MSYS2 prompt:

pacman -Syu

Close terminal, then reopen:

pacman -Su

repeat a few times until everything appears stable.

MSYS2 components

Select the “all” option (default).

pacman -S zip git  base-devel mingw-w64-x86_64-ninja \
              mingw-w64-x86_64-toolchain \
              mingw-w64-x86_64-cmake \
              mingw-w64-x86_64-extra-cmake-modules \
              automake gcc-fortran

Mantis

Note - some of the build tools issue complaints about path lengths, so carry out the build somewhere near the top of the drive and move it to the spm/toolbox folder later.

All the following commands are executed from the MSYS2 shell.

Fetch mantis (as per linux etc):

git clone https://github.com/DevelopmentalImagingMCRI/mantis.git
cd mantis
git submodule init
git submodule update

Create the build folder. PCWIN64, in the paths below, is the result of the matlab command:

computer

Change it if you get a different response on your system.

cd mantis/ITKStuff
mkdir Build.PCWIN64
cd Build.PCWIN64

Set the msys path

export PATH=/c/msys64/mingw64/bin:$PATH

Configure the build:

cmake -G Ninja \
-DCMAKE_CXX_COMPILER=c:/msys64/mingw64/bin/c++.exe \
-DCMAKE_EXE_LINKER_FLAGS="-static-libgcc -static-libstdc++ -static -lpthread"  \
../SuperBuild

Run the build:

ninja

Wait….

When it is done, check that the executables run by double clicking on them from explorer. Exe files will be in

mantis/ITKStuff/Build.PCWIN64/MANTiS-build/bin/

Nothing should happen, but if there is an error message about missing libraries, then something has gone wrong.

Drag the entire mantis folder structure into the spm/toolbox folder.

Give it a try.