bughht / Flow-Bloch-T1-mapping-cpp

A C++ implementation of the Bloch simulator for T1 mapping

T1 mapping Bloch Simulator

Introduction

This is a C++ implementation of the Bloch simulator for T1 mapping. It includes the following modules:

• Bloch simulation
• b-SSFP sequence generation and simulation
  • k-space sampling and image reconstruction
• MOLLI sequence generation and simulation
• Flow phantom simulation
• T1 fitting

This project was originally transplanted from FLOW-BLOCH-T1-MAPPING for higher performance. Now it's a standalone project.

Project Structure

• src contains the source code of the simulator.
  • BlochSim contains the Bloch simulation code.
  • FlowPhantom contains the flow phantom simulation code.
  • M_voxel contains the magnetization vector class.
  • SeqLoader contains the sequence loader code.
  • SeqSimulator contains the sequence simulator code.
  • main.cpp is the main function.
• python contains the python scripts.
  • GenSeq_MOLLI.py generates the MOLLI sequence.
  • GenSeq_SSFP.py generates the b-SSFP readout sequence.
  • load_cppimg.py loads the image generated by the simulator.
  • MOLLI_fit.py contains the fit algorithm.
  • T1_fit.ipynb fits the T1 data and display the result.
• test contains the test code.
• build is the build directory, executables will be generated here.
• run.py enables parallel execution of the simulator, temporarly for experiments.

Features

• Sequence generator and T1-fitting are implemented in Python with Numpy and Scipy.
• The sequence simulator is implemented in C++ for higher performance.
• Matrix computation in Bloch simulation is accelerated by Eigen3.
• Parallel computation in k-space sampling and flow phantom simulation is accelerated by OpenMP.
• OpenCV is used for MRI image reconstruction.

Prerequisites

• CMake >= 3.0
  • OpenCV
  • Eigen3
  • OpenMP >= 4.5.0
• Python >= 3.7
  • numpy
  • scipy
  • matplotlib
  • pyyaml
  • ruamel.yaml
  • tqdm
  • ipynbcompress (Please build from personal manipulated source)

Build and Run

mkdir build
./cmake.sh
# Please set the parameters in run.py first.
# The default parameters are designed for experiments server with at least 32 processors and 64GB memory.
python run.py

TODO

• Bloch Simulation
• MOLLI sequence simulation
• K-space sampling & reconstruction
• Flow simulation
• Data Collection & Analysis
• Paper

License: GPL-2.0

FLOW-BLOCH-T1-MAPPING
Copyright (C) 2023  Haotian Hong

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.