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interfaces.slicer.converters

DicomToNrrdConverter

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/converters.py#L23

Wraps command ** DicomToNrrdConverter **

title:
Dicom to Nrrd Converter
category:
Converters

description: Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom header to extract necessary information about measurement frame, diffusion weighting directions, b-values, etc, and write out a nrrd image. For non-diffusion weighted dicom images, it loads in an entire dicom series and writes out a single dicom volume in a .nhdr/.raw pair.

version: 0.2.0.$Revision: 916 $(alpha)

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/Modules/DicomToNrrdConverter

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Xiaodong Tao

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.

Inputs:

[Mandatory]

[Optional]
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the interface fails to
        run
inputDicomDirectory: (an existing directory name)
        Directory holding Dicom series
outputDirectory: (a boolean or a directory name)
        Directory holding the output NRRD format
outputVolume: (a string)
        Output filename (.nhdr or .nrrd)
smallGradientThreshold: (a float)
        If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then
        DicomToNrrdConverter will display an error message and quit, unless the
        useBMatrixGradientDirections option is set.
useBMatrixGradientDirections: (a boolean)
        Fill the nhdr header with the gradient directions and bvalues computed out of the
        BMatrix. Only changes behavior for Siemens data.
useIdentityMeaseurementFrame: (a boolean)
        Adjust all the gradients so that the measurement frame is an identity matrix.
writeProtocolGradientsFile: (a boolean)
         Write the protocol gradients to a file suffixed by ".txt" as they were specified in the
        procol by multiplying each diffusion gradient direction by the measurement frame.  This
        file is for debugging purposes only, the format is not fixed, and will likely change as
        debugging of new dicom formats is necessary.

Outputs:

outputDirectory: (an existing directory name)
        Directory holding the output NRRD format