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README.md

  1. License ==========

See LICENSE file for licensing information.


The tools in this software implement various reconstruction algorithms for Magnetic Resonance Imaging. The software is intended for research use only and NOT FOR DIAGNOSTIC USE. It comes without any warranty (see LICENSE for details).

Please cite the corresponding articles when using these tools. Some references can be found at the end of this file. The source code might provide more detailed references, e.g. for specific iterative algorithms.

  1. Help =======

Please direct all questions or comments to the public mailing list:

mrirecon@lists.eecs.berkeley.edu

https://lists.eecs.berkeley.edu/sympa/info/mrirecon

Note: This list has a public archive! Please do not send any confidential information.

Updates and further information can be found here:

http://mrirecon.github.io/bart/
  1. Installation ===============

2.1. Prerequisites

GCC compiler, the FFTW library, and optionally CUDA. (see recon/Makefile to turn options on or off)

The software can be used in combination with Matlab or octave.

There is limited support for reading Cartesian data encoded with the ISMRM Raw Data format when linking with the ISMRMRD library (http://ismrmrd.sourceforge.net/). Currently, BART only supports version 0.5.2 of this library. Later versions do not work.

In the following, the symbol '$' indicates a shell prompt. Do not type '$' when entering commands.

2.1.1. Linux

The software tools in recon should run on any recent Linux distribution.

To install the required libraries on Debian and Ubuntu run:

$ sudo apt-get install gcc make libfftw3-dev liblapack-dev libpng-dev

(optional)
$ sudo apt-get install octave

(optional)
install version 0.5.2 of the ISMRMRD library

2.1.2. Mac OS X

Xcode is required and it is recommended to install a newer version of gcc (4.7 seems to work) from MacPorts (http://www.macports.org/).

$ sudo port install fftw-3-single
$ sudo port install gcc47
$ sudo port install libpng

(optional)
$ sudo port install octave

(optional)
install version 0.5.2 of the ISMRMRD library

2.1.3. Windows

You can use BART on Windows using Cygwin:

https://www.cygwin.com/

Install Cygwin and select the following packages:

Devel: gcc, make
Math: fftw3, fftw3-doc, libfftw3-devel, libfftw3_3
Math: liblapack-devel, liblapack-doc, liblapack0
Libs: libpng, libpng-devel

Then use the cygwin shell to compile BART as described below.

(An alternative to using Cygwin is a virtual machine with Linux.)

2.2. Downloading and Compilation

If you are a git user, you can simply clone our public repository:

$ git clone https://github.com/mrirecon/bart

Otherwise, please download the latest version as a zip file from Github:

http://github.com/mrirecon/bart/releases/latest

and unpack it somewhere on your computer.

Open a terminal window and enter the bart directory (the top-level directory with the Makefile in it). To build the reconstruction tools type:

$ make

If you have installed the ISMRMRD library version 0.5.2, you can also build the ISMRM raw data import tool:

$ make ismrmrd

2.3. Getting Started

2.3.1. Organization

.           main directory / built software tools
Makefile    Makefile
matlab/		Matlab helper scripts
python/		Python helper functions
doc/		documentation
src/		source code
src/calib 	source code for sensitivity calibration
src/sense	source code for SENSE or ESPIRiT reconstruction
src/noir	source code for nonlinear inversion
src/sake	source code for SAKE reconstruction
src/wavelet2	source code for wavelets
src/wavelet3	source code for new wavelets (experimental)
src/num		base library with numerical functions
src/iter	iterative algorithms
src/linops	library of linear operators
src/misc	miscellaneous (e.g. I/O)
src/ismrm	support for ISMRM raw data format
lib/		built software libraries

2.3.2. Terminal

When using the toolbox commands from a UNIX shell, it is recommended to set the TOOLBOX_PATH to the base directory and to add it to the PATH variable. You can do this by running the following command:

$ . vars.sh

Note: The dot or 'source' command is needed so that the variables are imported into the current shell.

2.3.3. Matlab

You can set the TOOLBOX_PATH to the base directory and to add it to the Matlab path by running the following command in the bart directory:

>> vars

(Note: The '>>' indicates the shell prompt. Do not type '>>' when entering commands.)

You can use Matlab to read and visualize/process files. To write a data file 'xyz' from Matlab you can run:

>> writecfl('xyz', A);

Note, that the name 'xyz' is used without filename extension. See below for more information about the file format used in BART.

To read the data file 'xyz' back into Matlab use:

>> A = readcfl('xyz');

To call a BART tool (e.g. ecalib) from Matlab, you can use the 'bart' command:

>> sensitivities = bart('ecalib', kspace);

Download and unpack the examples which demonstrate interoperability with Matlab. Go to the examples directory and run:

>> examples
  1. Data Format ==============

3.1. Generic

The input and output datasets are each stored in a pair of files: one header (.hdr) and one raw data (.cfl). The header is a simple text readable file that describes the dimensions of the data. The raw data file is a binary file containing a single contiguous block of array data of dimensions described in the header stored in column-major order (first index is sequential). The raw data file is complex float (32 bit real + 32 bit imaginary, IEEE 747 binary32 little-endian).

Convenience methods to read and write our data files using Matlab may be found in recon/matlab (readcfl.m and writecfl.m).

3.2. Magnetic Resonance Imaging Data

For MRI data and images, the dimensions are usually assigned in the following order:

0 readout
1 phase-encoding dimension 1
2 phase-encoding dimension 2
3 receive channels
4 ESPIRiT maps
...
...

(more dimensions are defined in src/misc/mri.h)

Undersampled data is stored with with zeros in the unsampled positions.

3.3. Non-Cartesian Trajectories and Samples

The k-space coordinates for each sample are stored along dimension 0 which must have size equal to three. The unit of measurement is 1/FOV. Dimension 1 stores the samples along a single readout windows while dimension 2 may be used to differentiate between different lines (e.g. radial spokes). Channel (3) and map (4) dimensions must not be used (i.e. have size one), while other dimensions can be used as for Cartesian data. Non-Cartesian samples are stored in a similar way as trajectories except that dimension 0 is not used. The channel dimension can be used for different receiver coils as usual.

  1. Command-line Tools =====================

All tools operate on the simple file format given above. Indices and dimensions run from 0 to N-1. Sometimes a set of dimensions is given as a bitmask where the lowest bit corresponds to the 0st dimension.

For example, an inverse Fourier transform of first three dimensions can be performed with the following command:

$ bart fft -i 7 kspace volume

More information about each command can be found in 'doc/commands.txt'.

  1. References =============
  • Uecker M, Ong F, Tamir JI, Bahri D, Virtue P, Cheng JY, Zhang T, Lustig m, Berkeley Advanced Reconstruction Toolbox, Annual Meeting ISMRM, Toronto 2015 In: Proc Intl Soc Mag Reson Med 23:2486

  • Uecker M, Virtue P, Ong F, Murphy MJ, Alley MT, Vasanawala SS, Lustig M, Software Toolbox and Programming Library for Compressed Sensing and Parallel Imaging, ISMRM Workshop on Data Sampling and Image Reconstruction, Sedona 2013

References related to implemented methods and algorithms can be found in the file 'doc/references.txt'.

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