BET2 - Brain Extraction Tool

BET2 is a brain extraction tool designed to remove non-brain tissue from images of the whole head. It can also estimate inner and outer skull surfaces as well as the outer scalp surface if high-quality T1 and T2 input images are available. This guide will walk you through the process of compiling and executing the BET2 project on an ARM-compatible device.

For more information about BET and related tools, visit the FMRIB Software Library (FSL) website: FSL Git RepositoryAdditionally, you can explore the modified version of BET with added features on another GitHub repository: GitHub - liangfu/bet2. You can also find additional resources and documentation on BET on the FSL wiki page: BET Documentation.

Clone the Repository

Begin by cloning the project repository from GitHub onto your local machine. You can do this by running the following command in your terminal or command prompt:

git clone https://github.com/Bostrix/FSL-BET2.git

This command will create a local copy of the project in a directory named "FSL-BET2".

Navigate to Project Directory

Change your current directory to the newly cloned project directory using the following command:

cd FSL-BET2

This command ensures that you are working within the project directory for any subsequent actions.

Installation of Development Tools and Libraries

To set up the necessary development environment on your ARM device, follow these steps:

• Install the essential development tools, compilers, and libraries by running the following commands:

sudo apt install build-essential
sudo apt install gcc-aarch64-linux-gnu
sudo apt  install cmake
sudo apt install make

These commands will install the required packages for building and compiling code on the ARM architecture.

Compilation with CMake

To compile Bet and generate the necessary Makefiles using CMake, Use the following command:

mkdir build
cd build
cmake ..
make

Successful Compilation and Execution

After making necessary changes, recompile the project to ensure that the modifications were applied correctly. The executable file, in this case "bet2", will be created in the "bin" directory specified in the CMakeLists.txt file. To test the functionality of the program, execute the "bet2" executable by providing input and output files. For example:

cd ../bin
./bet2

Execute the ./bet2 command with the required input file and output file options. Here is the basic syntax:

./bet2 <input_fileroot> <output_fileroot> [options]

Replace <input_fileroot> with the path to your input file and <output_fileroot> with the desired output file name.You may optionally specify one or more of the following arguments to customize the behavior of BET2. During execution, the program performs 1000 iterations as part of its processing. Upon completion, it generates the specified output file.

Conclusion

You have now successfully compiled and executed the BET2 project on your ARM-compatible device. Follow the provided instructions to compile the project with CMake and run the executable with the desired input and output files. If you encounter any issues or have further questions, refer to the project documentation or seek assistance from the project maintainers. Happy brain extraction!