Documentation/4.2/Modules/DicomToNrrdConverter

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Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Jim Miller, GE
Contact: Jim Miller

NA-MIC  
GE  
Itk  

Module Description

Use Cases

This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer4 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

Supported DWI formats:

  • Philips scanner/software version combinations:
    • Achieva 2.1.3.6
    • Achieva 2.5.3.0
    • Achieva 2.5.3.3
    • Achieva 2.6.1.0
    • Acheiva 2.6.3.4
    • Intera 2.1.3.6
    • Intera 2.6.3.5
  • Siemens
    • Trio B13
    • Trio B15
    • Trio B17
    • Verio B15V
  • GE
    • SIGNA HDx14.0
    • SIGNA HDxt 15.0
    • DVMR 20.0M4
    • DVMR 20.1

Usage

A command line example for running the module is:

DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr

The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the smallGradientThreshold flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.

For Siemens data: In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the useBMatrixGradientDirections flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the bMatrix DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the 3x3 unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.

Panels

Parameters:





     * '
     
       ** ': 
     
   
 


Screenshot of the UI

Tutorials

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Similar Modules

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References

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