youngwook-mri / ox-bart

BART interoperability with GE Healthcare's Orchestra library

Ox-Bart conversion tools

Library and converter tools for interop between BART and GE Healthcare's Orchestra.

If you can build bart and you can build the orchestra-sdk examples, you should be able to build these tools.

These tools are intended for research purposes only and come with no warranty. These tools are NOT FOR DIAGNOSTIC USE. See LICENSE for details.

These tools use the GE Orchestra API. The Orchestra SDK is copyright GE Healthcare

Requirements

• Tested with BART v0.3.01, v0.4.01, (and up to commit 5ea0a5a). Currently does not support CUDA builds (trivial fix)
• Tested with Ox v1.8 (older versions not currently supported)
• Requires cmake 3.6 or higher

Building

Must have BART installed without CUDA

Set TOOLBOX_PATH to the top-level BART directory, e.g.

export TOOLBOX_PATH=/home/jtamir/bart

Set OX_INSTALL_DIRECTORY to the top-level Orchestra sdk directory, e.g.

export OX_INSTALL_DIRECTORY=/home/jtamir/orchestra-sdk

Build the tools with

./build.sh

The tools and libraries can be found under bin/ and lib/

Usage

PfileToBart

Use to convert a Pfile to a BART cfl/hdr file.

Usage: PfileToBart [options] --pfile <Pfile> --output <kspace>

Write <Pfile> data into BART-formatted file <kspace>.
--fft flags performs an FFT on the data along flags
--ifft flags performs an IFFT on the data along flags
--fftmod flags performs an FFTMod on the data along flags
--weights <file> output channel weights to <file>

BartToDicom

Takes a Pfile and a bart kspace file, and generates Dicoms using the Ox Dicom chain, e.g. gradwarp, resizing, etc.

Usage: BartToDicom [options] --pfile <Pfile> --input <kspace>

Write BART-formatted data in <kspace> to dicom using Pfile info.
--fft flags performs an FFT on the data along flags
--ifft flags performs an IFFT on the data along flags
--fftmod flags performs an FFTMod on the data along flags
--weights <weights> inputs custom channel weights

NoiseCov

Usage: NoiseCov --input <NoiseStatistics> --covar <covar> --noise <noise> --optmat <optmat>

Write noise data and covariance matrix files to BART-formatted data

CalibrationData

Usage: CalibrationData --pfile <Pfile> --input <RawCalibration> --body <body_coil> 

Write body coil pre-scan h5 data into BART-formatted file based on dimensions in <Pfile>