bmcppfit is a (work-in-progress) flexible standalone, multi-thread, Bloch-McConnell fit application. It was developed next to Pulseq-CEST and is compatible with the pulseq-cest simulation setting files. As the C++ simulation code is very similar, bmcppfit might be merged to the Pulseq-CEST project at some point.
bmcppfit can be called from the command line with a fit parameter yaml-file as input:
bmcppfit -p="parameter_file.yaml" -o="results.yaml"
A detailled description of the parameters etc can be found in the subfolder Readme
You can either download the latest pre-compiled binaries from the GitHub workflow or Releases, use docker or install it locally.
You can pull the latest image from dockerhub:
docker pull kherz/bmcppfit:latest
Afterwards, enter the container with a mounted tmp folder:
docker run --rm -it -v /tmp:/tmp kherz/bmcppfit
You can now use the container and save intermediate data in /tmp. You can run the example with:
/opt/code/bmcppfit/install/bin/bmcppfit -p=/opt/code/bmcppfit/tests/matlab/FP_GM_3T_001_bmcppfit.yaml -o=/tmp/fit_results.yml
The fit results are now in /tmp/fit_results.yml
- A compiler with at least C++ 14 standard
- Git
- CMake >= 3.16
- vcpkg (If not installed, please follow the steps below. Otherwise continue here)
Clone the vcpkg repository
git clone https://github.com/microsoft/vcpkg
Then depending on your OS, run:
./vcpkg/bootstrap-vcpkg.sh
.\vcpkg\bootstrap-vcpkg.bat
For windows, the standard architechture is x86. It is recommended to change the default to x64 on 64 bit systems by setting the environment variable:
VCPKG_DEFAULT_TRIPLET=x64-windows
See vcpkg installation guide for more details.
Clone the repository:
git clone https://github.com/kherz/bmcppfit
and prepare build directories:
cd bmcppfit
mkdir build
Configure CMake (will take a while if vcpkg packages need to be built):
cmake -B build -DCMAKE_TOOLCHAIN_FILE=${PATH_TO_VCPKG_INSTALLATION}/vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Release
Run the build process:
cmake --build build --config Release
Run install to copy the binary and dependencies to the install directory
cmake --install build --prefix install
The binaries are now in bmcppfit/install/bin.