update

Author: aghaeifar

README.md

@@ -60,16 +60,16 @@ We recommend using the provided Dockerfile, which automates the installation of
 
 ```shell
 git clone https://github.com/aghaeifar/SpinWalk
-cd containers
+cd SpinWalk/containers
 docker build --no-cache -t spinwalk ..
 docker run --gpus all --rm -it --runtime=nvidia spinwalk bash
 ```
 #### CMake
 
-**Dependencies**
+**Dependencies:**
 
 - 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.
+- 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#id5)). 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)
@@ -82,6 +82,7 @@ git clone https://github.com/aghaeifar/SpinWalk.git
 cd SpinWalk
 cmake -B ./build
 cmake --build ./build --config Release
+sudo cmake --install ./build
 ```
 ---
 
@@ -102,7 +103,14 @@ spinwalk sim -c config1.ini config2.ini ...
 ---
 ### Configuration files
 
-Configruation file is a text based [ini file](https://en.wikipedia.org/wiki/INI_file) used to provide simulation parameters for simulator. Simulator can accept more than one configuration to simulation several configurations. A configuration file can inherit from another configuration file to avoid writing repetitive simulation parmeters. All the possible parameters are provided in [config_default.ini](./config/config_default.ini) with definition and expected unit.
+The configuration file is a text-based [INI file](https://en.wikipedia.org/wiki/INI_file) used to specify simulation parameters for SpinWalk. SpinWalk can process multiple configuration files to simulate various setups. A configuration file can inherit parameters from another configuration file to avoid duplicating repetitive simulation settings.  
+
+All possible parameters are documented in [config_default.ini](./config/config_default.ini), along with their definitions and expected units.  
+
+- The `config` subcommand can be used to generate configuration files for some popular sequences. These auto-generated files may require further modifications to suit specific purposes. 
+- The `dwi` subcommand allows adding diffusion gradients to an existing configuration file.  
+
+For a demonstration, refer to the [free diffusion](./demo/spinwalk_dwi.ipynb) example.  
 
 ---
 ### Input/Output file format

demo/spinwalk_dwi.ipynb

@@ -84,11 +84,11 @@ int main(int argc, char * argv[])
     subcommand_config->add_option("-t,--timestep", timestep_us, "timestep in \u00B5s")->mandatory(true)->check(CLI::PositiveNumber);; 
     subcommand_config->add_option("-o,--output",config_file, "Path to save the configuration file")->mandatory(true);
 
-    auto subcommand_diffgrad = app.add_subcommand("dMRI", "Generate diffusion gradient table");
-    subcommand_diffgrad->add_option("-b,--bvalue", bvalue, "b-value(s) as many as you want. e.g. -b 100 500 1000 5000 (s/mm\u00B2)")->mandatory(true);
-    subcommand_diffgrad->add_option("-v,--bvector", bvector, "Gradient direction: X Y Z, e.g. 0.267 0.534 0.801")->mandatory(true)->expected(3);
-    subcommand_diffgrad->add_option("-d,--delta", bdelta, "start time, \xCE\xB4 and \xCE\x94 in ms, e.g. 10 3 5 ")->mandatory(true)->expected(3);
-    subcommand_diffgrad->add_option("-c,--config", config_file, "input config file to insert PGSE gradients and excitation and refocusing RF")->mandatory(true)->check(CLI::ExistingFile);
+    auto subcommand_diffusion = app.add_subcommand("dwi", "Generate diffusion gradient table");
+    subcommand_diffusion->add_option("-b,--bvalue", bvalue, "b-value(s) as many as you want. e.g. -b 100 500 1000 5000 (s/mm\u00B2)")->mandatory(true);
+    subcommand_diffusion->add_option("-v,--bvector", bvector, "Gradient direction: X Y Z, e.g. 0.267 0.534 0.801")->mandatory(true)->expected(3);
+    subcommand_diffusion->add_option("-d,--delta", bdelta, "start time, \xCE\xB4 and \xCE\x94 in ms, e.g. 10 3 5 ")->mandatory(true)->expected(3);
+    subcommand_diffusion->add_option("-c,--config", config_file, "input config file to insert PGSE gradients and excitation and refocusing RF")->mandatory(true)->check(CLI::ExistingFile);
 
     CLI11_PARSE(app, argc, argv);
     if(app.count_all() == 1){
@@ -113,7 +113,7 @@ int main(int argc, char * argv[])
     std::cout << "Log file location: " << std::filesystem::current_path() / log_filename << '\n';
 
     // ========== generate diffusion gradients ==========
-    if (subcommand_diffgrad->parsed())
+    if (subcommand_diffusion->parsed())
         if (dMRI::handler::execute({.start_ms=bdelta[0], .delta_ms=bdelta[1], .DELTA_ms=bdelta[2], .dir=bvector, .b_value=bvalue, .output=config_file}) == false){
             std::cout << ERR_MSG << "Diffusion gradient generation failed. See the log file " << log_filename <<", Aborting...!" << "\n";
             return 1;