uTIlzReg Files

DISCLAIMER:

This software has been developed for research purposes only, and hence should not be used as a diagnostic tool. In no event shall the authors or distributors be liable to any direct, indirect, special, incidental, or consequential damages arising of the use of this software, its documentation, or any derivatives thereof, even if the authors have been advised of the possibility of such damage. 


INFORMATION:

uTIlzReg is a set of light programs to perform diffeomorphic registration of 2D/3D images (plus useful tools). It is written in C++ and can be easily compiled using CMake. It works with non-compressed nifti images (.nii). 

Much further information is available at    http://laurent.risser.free.fr/uTIlzReg/menu_uTIlzReg.html


DEVELOPERS:
Laurent Risser, PhD - Imperial College London (2009-2010), University of Oxford (2011), CNRS / Institut de Mathématiques de Toulouse (2012 - .)
Francois-Xavier Vialard, PhD - Imperial College London (2009-2011), Universite Paris Dauphine (2011 - .)




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#1) COMPILING uTIlzReg  (LINUX & MAC / equivalent procedure with WINDOWS)
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#To Compile, you can use the following command lines from here:

mkdir utilzreg_BUILD
cd utilzreg_BUILD
cmake -g ..
make
cd ..


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#2) USING DIFFERENT TOOLS OF uTIlzReg
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#To test the code, you can then use the following command lines from here. Note that the results presenting shape evolutions are saved in 3D+t images. Such deformations can be seen using, e.g., rview from irtk (http://www.doc.ic.ac.uk/~dr/software/). We also recommend to use itksnap (http://www.itksnap.org) to visualize 3D images (but not 3D+t as far as we know).

#2.1) Variables definition and directory to store the results.

ureg_LDM="./utilzreg_BUILD/uTIlzReg_LDDMM"
ureg_GS="./utilzreg_BUILD/uTIlzReg_GeoShoot"
ureg_LD="./utilzreg_BUILD/uTIlzReg_Demons"
mkdir utilzreg_RESULTS

#2.2) Perform LDDMM registration with large deformations using the sum of different kernels [Risser et al, TMI 2011]. Results are saved in "./utilzreg_RESULTS/potatoReg_LDDMM*".

$ureg_LDM ./DATA/Potato2D_Src.nii ./DATA/Potato2D_Trg.nii -PrefixOutputs ./utilzreg_RESULTS/potatoReg_LDDMM -iterations 200 -subdivisions 30 -M_Gauss_easier 2 15 -symmetric -FinalDefVec -FinalDefInvVec

#2.3) Perform Geodesic Shooting registration on 3D images [Vialard et al, IJCV 2011]. Results are saved in "./utilzreg_RESULTS/BrainReg_GS*".

$ureg_GS ./DATA/Brains3D_4mm_Src.nii ./DATA/Brains3D_4mm_Trg.nii -PrefixOutputs ./utilzreg_RESULTS/BrainReg_GS -iterations 20  -M_Gauss_easier 4 10 -OutFinalDef -OutDispField -OutDeformation

#2.4) Perform LogDemons registration on 3D images (adapted from [Vercauteren et al., MICCAI 2008] with the kernels of [Risser et al, TMI 2011]). Results are saved in "./utilzreg_RESULTS/BrainReg_LD*".

$ureg_LD ./DATA/Brains3D_4mm_Src.nii ./DATA/Brains3D_4mm_Trg.nii -PrefixOutputs ./utilzreg_RESULTS/BrainReg_LD -iterations 20   -MK_fluid 3 4 7 10


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#3) WEBSITE WITH ADDITIONAL INFORMATION
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#More info at: http://laurent.risser.free.fr/uTIlzReg/menu_uTIlzReg.html


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#4) PARALLELIZATION USING OPENMP
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#To make possible parallel computations using openmp:
#-> In [utilzreg]/CMakeLists.txt:            uncomment the line "#set(CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -fopenmp")"  
#-> In [utilzreg]/lib/src/CMakeLists.txt:    uncomment the line "#set(CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -fopenmp")"  
#-> In [utilzreg]/lib/include/SciCalcPack.h: replace "//define COMPILE_WITH_OPENMP"  with  "#define COMPILE_WITH_OPENMP"
#-> In [utilzreg]/lib/include/SciCalcPack.h: replace "//include <omp.h> "  with  "#include <omp.h> "
#-> Then (re)construct the makefile or equivalent using cmake