Free Software

DEVELOPED AND MADE AVAILABLE WITH SUPPORT FROM
The NIH National Institute of Biomedical Imaging and Bioengineering

Spiral MRI Pulse Sequence
An MRI pulse sequence with spiral read-out gradients and image reconstruction code. The sequence is written in GE's EPIC pulse programming environmenmt and is available in precompiled format for 5.x and LX platforms. The reconstruction software is precompiled C code. You need to have a GE research agreement to be able to run the sequence on your scanner. To obtain this package, please send email to Gary Glover (gary@lucas.stanford.edu) stating your name, research institute, and scanner software version (the output from the command "whatRev" run on your scanner host will tell you this information). A licensing agreement (which needs to be signed and faxed back) and instructions for downloading this software package will be sent to you.
Diffusion Tensor Image Post-Processing
Post-processing routines for reconstruction of diffusion tensor images. Precompiled binaries for Unix/Linux are available. Please send email to Mike Moseley (mike@lucas.stanford.edu) stating your name and research institute. Instructions for downloading this software package will be sent to you. For more details, visit http://rsl.stanford.edu/moseley/tensorcalc
RF Pulse Design
A library of Matlab routines developed by John Pauly (pauly@mrsrl.stanford.edu) for designing RF pulses using the Shinnar-Le Roux algorithm. Reference: Pauly J, Le Roux P, Nishimra D, Macovski A. Parameter relations for the Shinnar-Le Roux selective excitation pulse design algorithm. IEEE Tr Medical Imaging 1991; 10(1):53-65. Also available is the dualband RF pulse described in: Schricker AA, Pauly JM, Kurhanewicz J, Swanson MG, Vigneron DB. Dualband spectral-spatial RF pulses for prostate MR spectroscopic imaging. Magn Reson Med 2001;46:1079-87. The following software package developed by Adam B. Kerr and Peder E.Z. Larson includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application in magnetic resonance spectroscopy and imaging. See the "examples/" folder for sample code and pulse designs. This package depends on the rf_tools library of Matlab routines listed above. The following references describe the design methods used:
- Kerr, A.B., Larson, P.E., Lustig, M., Cunningham, C.H., Chen, A.P., Vigneron, D.B., and Pauly, J.M. Multiband spectral-spatial design for high-field and hyperpolarized C-13 applications. In Proceedings of the 16th Annual Meeting of ISMRM (Toronto, 2008), p.226.

- Larson, P. E.Z., Kerr, A.B., Chen, A.P., Lustig, M., Zierhut, M.L., Hu, S., Cunningham, C.H., Pauly, J.M., Kurhanewicz, J., and Vigneron, D.B. Multiband excitation pulses for hyperpolarized 13C dynamic chemical shift imaging. J Magn Reson 194, 1 (Sept. 2008), 121-127.
  • Download Matlab library: ss.zip
The MATLAB file ABS.mat below includes a complex 6-ms RF pulse for use in a Bloch-Siegert B1 mapping sequence. The pulse was designed using the method described in Adiabatic RF pulse design for Bloch-Siegert B1+ mapping. Mohammad Mehdi Khalighi, Brian K. Rutt and Adam B. Kerr Magnetic Resonance in Medicine DOI: 10.1002/mrm.24507. The MATLAB file also includes a lookup table to go from the measured Bloch-Siegert phase shift and off-resonance B0 to the |B1| transmit field magnitude. A "help" string is included in the MATLAB file which describes the contents and use in more detail.
Tools for GE MR Data
Software developed by Marcus Alley (mtalley@stanford.edu). These are all binary programs (so you might have to make them executable after download) that run from a command window.
  • rdgehdr prints the entire header of any GE image (non-DICOM, i.e., 9.x or earlier) or raw data file.
       GE 11.x and earlier :: cygwin | sgi | sunos
       GE 5.x - 16.x, 20.x - 24.0 V01 :: linux 32-bit | linux 64-bit | mac 10.8 | windows
  • addimghdr adds a GE image header to a header-less image. Supported formats include 5.x/LX/DICOM. This routine requires the header of the raw data file ("Pfile") that generated the image.
       GE 11.x and earlier :: sgi | cygwin
       GE 5.x - 16.x, 20.x - 24.0 V01 :: linux 32-bit | linux 64-bit | mac 10.8
Software developed by Thomas Brosnan (brosnan@stanford.edu):
  • dcm2gen converts from DICOM to GE Genesis 5.x image file format (MR images only).
       windows | linux | mac osx
  • printraw displays entire header of GE raw data files ("Pfiles").
       linux | mac osx