Software

SVRTK toolbox

We have created a new SVRTK toolbox where we are collecting our reconstruction algorithms for fetal MRI. Please follow the link bellow for instructions how to install the software

github.com/SVRTK/SVRTK

Previous versions

irtk-simple

Motion correction and super-resolution reconstruction of structural fetal brain MRI

The latest version of reconstruction software is available here:

gitlab.com/mariadeprez/irtk-simple

It has been updated to be easier to compile on Ubuntu systems and is now parallelised by default. The TBB library is included to ensure compatibility.

Installation

Instructions for installation on Ubuntu systems

First we need to make sure that all the packages needed, including git and cmake, are installed on your machine. Run

sudo apt-get install git cmake cmake-curses-gui g++ zlib1g-dev

Download irtk-simple:

git clone https://gitlab.com/mariadeprez/irtk-simple.git

Compile:

cd irtk-simple

mkdir build

cd build

cmake ..

make -j

The viewer (rview) has been disabled in this version to make the compilation easier. The viewer can be downloaded from here: https://www.doc.ic.ac.uk/~dr/software/download.html

Running the motion correction software

The motion correction and super-resolution slice-to-volume reconstruction is implemented in executable

reconstruction

The full path is your_path/irtk-simple/build/bin/reconstruction

Just run it on the command line to get help. It takes nifti images (.nni or .nii.gz) which should be stacks of slices approximately aligned in world coordinate system. Use of mask is strongly recommended, though for neonatal data (or paediatric or adult), the option

-remove_black_background can be used instead to mask the image automatically.

If you use the reconstruction software, please reference it as

"Reconstruction of fetal brain MRI with intensity matching and complete outlier removal. M Kuklisova-Murgasova, G Quaghebeur, MA Rutherford, JV Hajnal, JA Schanbel. Medical Image Analysis 16(8), 2012"

About

The fetal brain slice-to-volume reconstruction was implemented as part of IRTK software package, originally developed by Prof. Daniel Rueckert from Department of Computing at Imperial College London. The original version of this software can be downloaded and compiled from

github.com/BioMedIA/IRTK

irtk-public

The latest version of reconstruction software is available at

https://gitlab.com/mariadeprez/irtk-public.git

However, it is only compatible with the libraries on Ubuntu 14.04 and not the newer versions. It requires VTK5 and older version of TBB that need to be linked using ccmake.

Download and compilation instructions are identical to the irtk-simple. Once the makefile is produced it need to be configured by running ccmake . and setting BUILD_WITH_TBB and BUILD_WITH_VTK ON. Paths to the VTK and TBB libraries then need to be set manually by pressing 't', setting the relevant variables, followed by pressing 'c' (configure), 'g' (generate), and running make.

The old version also supports reconstruction of fetal fMRI and various slice orders, including multi-band sequences.