Software

MatPulse

MATPULSE is a GUI-based program written in Matlab that enables calculation of Shinnar-LeRoux (SLR) frequency selective RF pulses. A description of an early version of the program is described in reference 1. The program also enables pulse re-mapping (the MATPULSE version of VERSE (2)), and includes a Bloch equations section, in addition to a variety of additional pulse manipulations and calculations, including gradient refocusing, and calculation of the effects due to relaxation. A number of analytical pulse shapes are also available, including sinc-Gauss and hyperbolic secant pulses. Over the years a number of additional features have been added to the original package, including pulse concatenation, root reflection (3), and the effects of flow.

MATPULSE is designed for Matlab 7 (release 14) running on Windows. Although the program should also run on earlier versions of Matlab, some options may be unavailable.

1. Matson, G.B. An integrated program for amplitude-modulated RF pulse generation and re-mapping with shaped gradients. Magn. Reson. Imaging 12, 1205-1225, 1994.
2. Conolly, s., Nishimura, D., Macovski, A., and Glover, G. Variable-rate selective excitation. J. Magn. Reson. 78, 440-477, 1988.
3. Pickup, S., and Xiaoning, D. Pulses with fixed magnitude and variable phase response profiles. Magn. Reson. Med 33, 648-655, 1995.

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MatCoil

MATCOIL is a GUI-based program written in Matlab that enables both single surface coils and surface coil configurations to be designed, and the resulting B₁ fields and sensitivity fields to be calculated and displayed. Additional parameters, such as tip angle, and vector field plots of the B₁ field, are also available. The coil shapes may be varied from circular, to elliptical, to rectangular, and may be planar or wrapped about a circular cylinder. In the present version of MATCOIL the coil configurations are co-axial. In addition, the present version of MATCOIL also enables a pair of circular coils to be designed and driven in quadrature, and the resulting B₁ fields to be displayed. Additional details of the program are available in the Word document MATCOIL.doc. The zipped file MATCOIL.zip is available for copying and downloading, and also contains the file MATCOIL.doc.

MATCOIL is designed for Matlab 7.0.1 (release 14) running on Windows. Although the program should also run on earlier versions of Matlab, some options may be unavailable.

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MatMRI

The MATMRI program is written in Matlab and calculates magnetization transfer (MT) effects based saturation of the bound pool as calculated and discussed by Henkelmann et al. and on the formulations for transfer of MT provided by Helms and Hagberg.

Brain

This program will identify the largest contiguous solid within an image, by applying erosion, threshholding, dilation and logical AND with the original threshold image. The program supports the HDF version 4.x *** format.

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DicomToHdf

This program converts Dicom data to HDF version 4.2 format. The program calls the windows command-line version of the dicom2 *** program for translation of the Dicom header. All dicom files growing from the parent directory are cataloged, and combined into a single HDF volume where possible. The program uses position vectors within each Dicom slice to verify slice ordering and data completeness.

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Segment

This program uses K-means cluster analysis to produce a 3 tissue classification on 3 channel MRI data. Expected inputs are a T1-Weighted image, and T2-weighted and a Pd-Weighted image. Initial cluster members are generated using histogram analysis of T1 data, and the clustering performed is identical to the SAS "Fastclus" procedure (circa 1992). HDF format supported.

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Sicore

This program transforms a classified MRI image down to the resolution of SI data, taking account of pulse and slice profiles, spatial response functions and metabolite shift. Values are reported in terms of tissue contribution per voxel. HDF format supported.

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Results

This program supports a broad range of processing on image data in the HDF format, including logical operations, rigid body transformations, format translations, and many other functions. The program is intended for batch processing of large data sets, primarily with non-interactive processing.

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Deformable Shape-Intensity Models (DSM)

DSM is a linear model. We used DSM to model the variation of the mean shape of the MR spectrum and mean intensity of the MR spectral images. By finding the transformation matrix and selecting the modes of variation representing the most information of the original MRSI we can reconstruct a new set of MRSI with much improved SNR. The current implementation was written in IDL and “C” for both interactive and batch processing

A complex valued DSM was used to improve signal to noise ratios (SNR) of multi-dimensional magnetic resonance spectroscopic imaging (MRSI) data sets without affecting spectral lineshapes and linewidths.

Import

Converts Siemens Vision system MR images (ACR-NEMA format) to HDF format.

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Talairach

Talairach registers T1-weighted images to the Talairach coordinate system. The images are first aligned such that the y-z plane passes through the interhemispheric fissure and the x-y plane passes through the user selected anterior and posterior commissures. A piecewise linear transformation is then used to transform the brain into Talairach space. Masks or regions of interest defined in Talairach space can also be transformed to aligned files, for automatic delineation of ROIs on individual brains.

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