diff --git a/README.md b/README.md index 7289aae..e419c55 100644 --- a/README.md +++ b/README.md @@ -166,7 +166,7 @@ h5write(filename, '/fov', fov); Multiple phantom files can be defined in the configuration file. Spinwalk will simulate them sequentially. -SpinWalk can also generate a digital phantom populated with cylinders or spheres. Details about the parameters are available in the help menu (execute *spinwalk -h*). +SpinWalk `phantom` subcommand can also generate a digital phantom populated with cylinders or spheres. Details about the parameters are available in the help menu (execute *spinwalk phantom -h*). #### M0 and XYZ0 [optional] @@ -191,7 +191,7 @@ The simulator generates a single output for each phantom. The output contains: - `M` : 4D single-precision floating-point array indicating the magnetization of spins at echo time(s). The dimentions are [scales, spins, echos, xyz (3)] - `T` : 4D 8-bit unsigned integer array indicating the tissue or object type where spins are located at the time of the echo. The dimentions are [scales, spins, echos, 1] - `XYZ` : 4D single-precision floating-point array indicating thethe spatial positions for either the entire random walk or just the final position. The dimentions are [scales, spins, steps, xyz (3)] -- `scales` : 1D double-precision floating-point array indicating scales used to scale the length/FoV of sample. +- `scales` : 1D double-precision floating-point array indicating scales used to scale the length/FoV of sample or gradients. The folder to save outputs can be specified in the configuration file. the filename pattern is *{seqname}_{phantom_file_name}.h5*, where *seqname* and *phantom_file_name* are both defined by user in the configuration file. @@ -205,6 +205,9 @@ scales = h5read(filename, '/scales'); T = h5read(filename, '/T'); T = permute(T, 4:-1:1); ``` + +Look at the provided demos for Python scripts. + ## Literature There are many nice papers published about simulation of BOLD signal in vessels network. A few are listed here for reference: