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mri_together_mrd

MRD data conversion tutorial @ MRI TOGETHER

https://mritogether.github.io/

Raj Ramasawmy @ NHLBI, NIH. Ahsan Javed @ NHLBI, NIH. Adrienne Campbell-Washburn @ NHLBI, NIH.

Contents

  • data
    • cartesian mrd
    • spiral mrd
    • siemens_raw_cartesian
    • ge_data_directory
    • bruker_data
  • python
    • simple cartesian reconstruction demo
  • matlab
    • spiral demo
  • shell
    • siemens_raw_data_conversion
    • example folder conversion

ISMRMRD Resources

Source Code

https://github.com/ismrmrd/ismrmrd https://github.com/ismrmrd/ge_to_ismrmrd https://github.com/ismrmrd/siemens_to_ismrmrd

ISMRMD API

https://ismrmrd.github.io/apidocs/1.5.0/

Publication

https://onlinelibrary.wiley.com/doi/10.1002/mrm.26089

Previous Video Tutorials

Introduction to MRD/ISMRMRD

https://www.youtube.com/watch?v=LhyqkNXdsoc

Data Conversion and editing

https://www.youtube.com/watch?v=ggauvF13-OM&t=592s

Installing

Quick Install Guide Videos

mrd-viewer

ismrmrd & siemens converter

Installation (everything)

  • note that this is installing things to the user home folder - you might want to change this!
  • This install creates a local directory for installed programs, which does not require sudo (but sudo is still required for package installations)
  • You will have to add the ~/local directory to your path, i.e. something like..
export ISMRMRD_HOME=~/local
export LD_LIBRARY_PATH=${ISMRMRD_HOME}/lib:${LD_LIBRARY_PATH}
export PATH=~/local/bin:~/local/usr/bin:${ISMRMRD_HOME}/bin:${PATH}

cd ~
mkdir local

sudo apt-get install g++ cmake git
sudo apt-get install libboost-all-dev xsdcxx libxerces-c-dev libhdf5-serial-dev h5utils hdf5-tools libtinyxml-dev libxml2-dev libxslt1-dev
sudo apt-get -y install doxygen git-core graphviz libboost-all-dev libfftw3-dev libhdf5-serial-dev

pip3 install ismrmrd gadgetron numpy matplotlib tabulate
pip3 install git+https://github.com/ismrmrd/ismrmrdviewer.git

git clone https://github.com/ismrmrd/ismrmrd.git
mkdir ismrmrd/build && cd ismrmrd/build
cmake -DCMAKE_INSTALL_PREFIX=~/local/ ..
make install

cd ../../
git clone https://github.com/ismrmrd/siemens_to_ismrmrd.git
mkdir siemens_to_ismrmrd/build && cd ismrmrd/build
cmake -DCMAKE_INSTALL_PREFIX=~/local/ ..
make install

Siemens MRI Cartesian conversion and Python recon

cd shell/
sh convert_siemens_data.sh
cd ../python/
python3 cartesian_demo.py

GE MRI Cartesian data conversion

To install ge2ismrmrd converter we need to install GE Orchestra on a linux distro with the correct libraries. We will be using a opensuse_15.2 image with orchestra installed for this demo. A more detailed installation with debuggin tips is available in the repo that is primarily maintained by Dr. Vinai Roopchansingh. (https://github.com/ismrmrd/ge_to_ismrmrd).

Please update the paths as needed in the install_ge_convertor.sh. We generally install in ~/local/ folder and thats what the install script would do as well.

cd shell/
sh install_ge_convertor.sh
source ~/.bashrc 
sh convert_ge_data.sh

Siemens Spiral conversion (c++) and Bruker Cartesian (julia) Matlab reconstruction

See matlab folder for some more examples.