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 . It can also simulate realistic variation of intensity. The whole pipeline and the simulation of variation of intensity are detailed in .
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:
 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
 Khanal, B., Ayache, N., & Pennec, X. (2016). Simulating Realistic Synthetic Longitudinal Brain MRIs with known Volume Changes. 2016. hal-01348959.
--with-clanguage=cxxoption when configuring PETSc.
First make sure that:
ITK_DIR. For example, I have my
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
simul@trophy with the following steps. I assume that you are inside a
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
cmake to build the files.
build$ cmake ..
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
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.