Simul@atrophy is a C++ based simulator tool that can simulate specified volume changes in different parts of the image. The tool was developed to generate synthetic time-series structural MRIs with specified ground truth atrophy. At its core, it implements a biophysical model of brain deformation with atrophy in Alzheimer’s disease detailed in [1]. It can also simulate realistic variation of intensity. The whole pipeline and the simulation of variation of intensity are detailed in [2].
The core components of the software are implemented in C++. It also contains a number of helper scripts (written in python) to preprocess input images and generate desired map of atrophy (or volume changes).
The following papers must be cited if you use this software:
[1] Khanal, B., Lorenzi, M., Ayache, N., & Pennec, X. (2016). A biophysical model of brain deformation to simulate and analyze longitudinal MRIs of patients with Alzheimer’s disease . NeuroImage , 134, 35–52. http://doi.org/10.1016/j.neuroimage.2016.03.061
[2] Khanal, B., Ayache, N., & Pennec, X. (2016). Simulating Realistic Synthetic Longitudinal Brain MRIs with known Volume Changes. 2016. hal-01348959.
--with-clanguage=cxx option when configuring PETSc.First make sure that:
--with-clanguage=cxx option.PETSC_DIR, PETSC_ARCH and ITK_DIR.
For example, I have my .bashrc with:
ITK_DIR=/home/bkhanal/Documents/softwares/ITK-build
export ITK_DIR
PETSC_DIR=/home/bkhanal/Documents/softwares/petsc
export PETSC_DIR
PETSC_ARCH=arch-linux2-cxx-debug
export PETSC_ARCH
Now, build simul@trophy with the following steps. I assume that you are inside a curr_dir, replace curr_dir with a directory of your choice.
curr_dir$ git clone https://github.com/Inria-Asclepios/simul-atrophy.git
curr_dir$ cd simul-atrophy
simul-atrophy$ mkdir build && cd build
Use cmake to build the files.
bash
build$ cmake ..
build$ make
If you have ITK installed with c++11, then use the following options with cmake:
build$ cmake -DUSE_CXX11:bool=true ..
build$ make
This should install the software to your machine.
The readme file details how to use the software.
The main simulator executable is build/src/simul_atrophy.
Running it with -h option alsow shows in detail the options available.
Otherwise, there is also a python script at ‘simul-atrophy/scripts/simul_atrophy.py’ which you can use.
Once again, use -h option to see the details.
Coming soon here.