update

README.md

@@ -22,38 +22,41 @@
 </div>
 
 
-SpinWalk is a Monte Carlo diffusion simulator. Spinwalk simulates spins (particles) random walk under a specific MR sequence within a digital phantom mimicing e.g., microvascular network, cells, axons, etc. 
+**SpinWalk** is a Monte Carlo diffusion simulator. It simulates the random walk of spins (particles) under a specific MR sequence within a digital phantom, which can represent structures such as microvascular networks, cells, axons, and more.
 
 ---
-### Key features
-- runs in GPU (massively parallel) or CPU
-- off-resonance: local field inhomogeneity because of susceptibility variation is accepted
-- T1 and T2 relxation times: Each substrate can have own relaxation defined
-- permeability: permeability between individual substrate can be defined with a probablity value
-- RF pulses: optinonal number of RF (with magnitude and phase)
-- Gradients: Gradient waveform in mT/m for each axis (X, Y, Z) can be defined
-- Recording trajectory of random walks in 3D
-- simulating steady state condition with given phase cycling and dummy scans
-- Boundry condition for crossing FoV
-- predefined or random spins placement 
-- predefined or equlibrium for initial spins magnetization
-- FoV can be internally scaled, allows simulating range of vessel size for BOLD fMRI contrast
+
+### Key Features
+- **GPU and CPU support**: Runs efficiently on both GPU (massively parallel) and CPU.
+- **Off-resonance effects**: Accounts for local field inhomogeneity due to susceptibility variations.
+- **T1 and T2 relaxation times**: Each substrate can have its own defined T1 and T2 relaxation times.
+- **Permeability**: Defines the permeability between individual substrates using a probability value.
+- **RF pulses**: Supports an optional number of RF pulses with specified magnitude and phase.
+- **Gradients**: Defines gradient waveforms in mT/m for each axis (X, Y, Z).
+- **Trajectory recording**: Tracks the trajectory of random walks in 3D space.
+- **Steady-state simulation**: Models steady-state conditions with given phase cycling and dummy scans.
+- **Boundary conditions**: Handles boundary conditions for crossing the field of view.
+- **Spin placement**: Allows predefined or random placement of spins.
+- **Initial magnetization**: Supports predefined or equilibrium initial spin magnetization.
+- **Field of View (FoV)**: The FoV can be internally scaled, enabling the simulation of a wide range of vessel sizes for BOLD fMRI contrast.
+
 
 ---
 ### Demo
 
-Jupyter notebooks that demonstrate the basic functionality of the SpinWalk for [BOLD fMRI contrast](./demo/spinwalk_example.ipynb) and [free diffusion](./demo/spinwalk_dwi.ipynb) simulation can be found in [demo](./demo) folder
+Jupyter notebooks demonstrating the basic functionality of SpinWalk for [BOLD fMRI contrast](./demo/spinwalk_example.ipynb) and [free diffusion](./demo/spinwalk_dwi.ipynb) simulations can be found in the [demo](./demo) folder.
 
-Here are example plots obtained from SpinWalk where show BOLD sensitivity as a function of vessel size for Gradient Echo (GRE) and Spin Echo (SE) seqeuences. Some [literature](#Literature) are provided as reference to get a better feeling of what are intended to get from this kind of simulations.
+Below are example plots generated by SpinWalk, showing BOLD sensitivity as a function of vessel size for Gradient Echo (GRE) and Spin Echo (SE) sequences. Some [literature](#Literature) is provided as a reference to help understand the intended outcomes of these simulations.
 
 ![](./docs/img/gre_se.jpg)
 
 ---
-### How to build
+### How to Build
+
 You can either use the supplied Dockerfile for a consistent build that includes all dependencies, or install the dependencies separately and compile using CMake.
 
-#### Docker 
-We suggest utilizing the provided Dockerfile, which automates the installation of all dependencies, as well as the cloning and building of the program. Clone SpinWalk and build using the provided [Dockerfile](./containers/Dockerfile) with:
+#### Docker
+We recommend using the provided Dockerfile, which automates the installation of all dependencies, as well as the cloning and building of the program. To build SpinWalk with the provided [Dockerfile](./containers/Dockerfile), clone the repository and run:
 
 ```shell
 git clone https://github.com/aghaeifar/SpinWalk
@@ -65,13 +68,13 @@ docker run --gpus all --rm -it --runtime=nvidia spinwalk bash
 
 **Dependencies**
 
-- A C++ compiler supprting C++20
-- CUDA toolkit newer than v12.0 that supports C++20 ([+](https://developer.nvidia.com/blog/cuda-toolkit-12-0-released-for-general-availability/)). Nvidia driver must support your CUDA release ([+](https://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html)). Check driver and cuda version with *nvidia-smi* and *nvcc --version* in terminal. 
+- A C++ compiler that supports C++20
+- CUDA toolkit version 12.0 or later that supports C++20 ([+](https://developer.nvidia.com/blog/cuda-toolkit-12-0-released-for-general-availability/)). Your Nvidia driver must support the corresponding CUDA version ([+](https://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html)). Check your driver and CUDA versions with *nvidia-smi* and *nvcc --version* in the terminal.
 - Boost libraries ([+](https://www.boost.org/))
-- HDF5 Library ([+](https://www.hdfgroup.org/downloads/hdf5))
-- Threading Building Blocks (TBB). 
-  
-If you prefer to install the program without using Docker, follow these steps (tested in Ubuntu 22.04):
+- HDF5 library ([+](https://www.hdfgroup.org/downloads/hdf5))
+- Threading Building Blocks (TBB)
+
+If you prefer to install the program without using Docker, follow these steps (tested on Ubuntu 22.04):
 
 ```shell
 sudo apt-get update && apt-get install -y libboost-all-dev libhdf5-dev libtbb-dev
@@ -84,7 +87,7 @@ cmake --build ./build --config Release
 
 ### How to simulate
 
-After building the program, simply launch `spinwalk` in the terminal to view the help menu with all available options. If a GPU is avaialbe and CUDA is installed, launch `spinwalk -g` to display GPU and driver version. SpinWalk has four subcommands. Subcommand `sim` is used for random walk simulations. The settings for simulation is provided through a configuration file. An example could be as:
+After building the program, simply run `spinwalk` in the terminal to view the help menu with all available options. If a GPU is available and CUDA is installed, you can run `spinwalk -g` to display the GPU and driver version. SpinWalk has four subcommands. The `sim` subcommand is used for random walk simulations. The settings for the simulation are provided through a configuration file. An example command might look like:
 
 ```shell
 spinwalk sim -c my_config.ini