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SPIN (signal processing in NMR) Software

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Over the last 5 years, our image processing group has developed our own stand alone software SPIN (signal processing in NMR) that operates with visual C++ on a windows based operating system. One of the reasons for this has been the special software we have been developing for susceptibility weighted imaging (SWI), perfusion weighted imaging (PWI) and MR angiography (MRA). Another has been because when we need certain features it is possible to generate them in the matter of weeks rather than months to a year as is usually required by other free software or commercially available software.

SPIN deals with the processing for a number of MRI sequences such as: SWI, PWI, MR angiography (MRA), dynamic contrast enhanced imaging (DCE), special image processing features such as interpolation and other mathematical operations, and special features for ease of use by clinicians. Specifically, the SWI module in SPIN makes it possible to combine magnitude and phase images and create minimum intensity maps over an arbitrary range of the tissue of interest. We also have new features (over and above what is offered in the Siemens SWI product for the 3T TRIO) for performing anti-aliasing and special processing of high pass filtered phase images. The MRA module offers a region growing algorithm to find the vessel tree starting from a specific vessel, and has the ability to simulate vessel flow. The PWI module provides cerebral blood volume (CBV), first moment mean transit time (fMTT), cerebral blood flow (CBF), bolus arriving time BAT), full-width half maximum estimates of MTT, time-to peak (TTP) and peak change in signal (PCS) images. All these maps are available in color coded images. The DCE module generates IAUC and CIAUC plots directly to a Microsoft Excel chart. SPIN also includes basic algorithms in imaging processing, such as subtraction, superimpositon, pixel division, averaging, offset shifting, edge detection, erosion, dilation, 2D parabolic fitting, sliding window filtering, complex thresholding, chirp-z transform dilation, and partial Fourier Transform processing.

SPIN can handle different image formats, including DICOM, Bruker raw/image files, Siemens raw images, graphic file types: jpeg, png, gif, bmp, tiff, SPM, Analyze,, Mricro and efilm. SPIN has a strong 3D view capabilities to display images in three orthogonal projections and manipulate ROI between different views, in addition, between individual images and MIP images, plus between different image sets. Data can be marked and viewed in 3D to isolate or segment structures of interest. SPIN uses a VTK package to do volume rendering, surface rendering, 3D MIP with full user interaction and rotating animations. SPIN can handle structural measurements in 3D, iron concentration measurements in SWI images, micro hemorrhage quantification and extraction from SWI data and cross-sectional area measurements in MRA.

Features:

SWI

  • Customized phase processing
    • Adjustable high pass homodyne filter
    • Anti-aliasing
    • Other techniques
  • Magnitude and phase multiplication
  • Minimum intensity projections
    • Background removal to preserve edges
    • With sliding window
  • Iron concentration measurements
  • Vein segmentation

PWI

  • Color indexed maps of
    • Cerebral blood volume (CBV)
    • First moment mean transit time (fMTT)
    • Cerebral blood flow (CBF)
    • Bolus arriving time (BAT)
    • Full-width half maximum estimates of mean transit time (MTT)
    • Time-to peak (TTP)
    • Change in signal (PCS)

MRA

  • Vessel Segmentation
    • Region growing
    • Global thresholding
    • Dynamic thresholding (by statistical analysis)
    • Shape filtering noise removal
  • 3D visualization
  • Cross-sectional area measurements

DCE

  • IAUC and CIAUC plots exported to Microsoft Excel

General Algorithms

  • Subtraction
  • Superimpose
  • Pixel division
  • Averaging
  • Offset shifting
  • Edge detection
  • Erosion dilation
  • 2D parabolic fitting
  • Sliding window filtering
  • Complex thresholding
  • Chirp-z transform dilation
  • Partial Fourier transform
  • Normalizing

3D Rendering with VTK

  • Maximum intensity projection (MIP)
  • Surface rending
  • Volume rending with adjustable transfer functions
  • Animation generation

Supported File Formats

  • Standard MRI
    • DICOM
    • Analyze
  • Graphic formats
    • JPEG
    • TIFF
    • PNG
  • 3D formats
    • VTK
    • SLC
  • Limited support
    • Siemens RAW
    • Bruker RAW

 

 

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