Add example test run with results and update readme

readme.md

@@ -49,7 +49,60 @@ This should install the software to your machine.
 The main simulator executable is `build/src/simul_atrophy`.
 Run with `-h` option to see in detail how to use it.
 
-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.
+### A basic example
+One very basic example of how to use simul@trophy is shown below on a relative small image so that this can be run quickly on a normal laptop/desktop.
+Note that if your image sizes are too large, usually greater than 120^3 you must use cluster computing for running the model due to memory limitations on normal desktops.
+Here I have used a dummy object instead of brain, but you can create your own test set by downsampling brain images too.
+Any file format readable by ITK will work; the example here uses `.mha` format.
+
+The input files and the results of this basic example can be found at the directory `basicExample`.
+
+There are three main input files:
+
+1. Input atrophy map: `test1Atrophy1.mha`
+
+1. Input segmentation file: `bMask.mha`
+
+1. Input image file: `bTest1.mha`
+
+The input parameters $\mu$ and $\lambda$ are set to 1 for both tissue and CSF regions.
+
+The example is run for two steps.
+
+```
+$build/src/simul_atrophy -parameters 1,1,1,1 -boundary_condition dirichlet_at_skull --relax_ic_in_csf -atrophyFile basicExample/test1Atrophy1.mha -maskFile basicExample/bMask1.mha -imageFile basicExample/bTest1.mha --invert_field_to_warp -numOfTimeSteps 2 -resPath ./basicExample/ -resultsFilenamesPrefix basicTest1_
+```
+
+If everything is all right you should be getting the following output in your display terminal:
+```
+Model will be run for 2 time steps
+dmda of size: (21,41,21)
+grid with the spacings hx, hy, hz: (1.000000,1.000000,1.000000)
+dirichlet_at_skull=>Skull velocity = 0.
+Incompressibility constraint relaxed where brain mask has label 1 
+Incompressibility constraint relaxation coefficient: 1/lambda.
+solver uses discretization for constant viscosity case!
+ muBrain=1.000000, muCsf=1.000000, lambdaBrain=1.000000, lambdaCsf=1.000000
+First Lame Parameter (lambda) is a scalar.
+
+ RHS will be taken as (mu + lambda)grad(a), i.e. with Lame parameters.
+
+ computing the operator for linear solve with 8 point stencil for divergence
+
+ Relax IC with div(u) + kp = 0 on relax cells
+
+ Displacement field inversion: tolerance not reached in 0 voxels 
+
+
+ Displacement field inversion: tolerance not reached in 0 voxels 
+```
+
+The output files created will be placed in the folder `basicExample`.
+The repository already contains the results of same example with prefix `basicTest_`.
+Now, after running this example you should get new files with the prefix `basicTest1_`.
+
+
+Instead of using the `simul_atrophy` executable directly, you can also a run the model by using the python script at 'simul-atrophy/scripts/simul_atrophy.py'.
+Please see `-h` option to see the details of the script.