Difference between revisions of "Modules:DicomToNRRD-3.4"

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[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 
[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 +
 +
[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
 
__NOTOC__
 
__NOTOC__
 
===Module Name===
 
===Module Name===
Dicom to NRRD converter for diffusion weighted imaging
+
DWI Dicom To NRRD
  
 
== General Information ==
 
== General Information ==
 
===Module Type & Category===
 
===Module Type & Category===
  
Type: CLI
+
Type: Command line module
 +
 
 +
Category: Converters
  
Category: Converter
+
{|
 +
|[[Image:DWIDicomToNrrdGUI.jpg|thumb|280px|Screenshot of the UI]]
 +
|}
  
 
===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
* Author: Xiaodong Tao (with contribution form Vince Magnotta)
+
* Author: Xiaodong Tao (with contribution from Vince Magnotta and Hans Johnson)
* Contact: taox at research . ge . com
+
* Contact: taox @ research.ge.com
  
 
===Module Description===
 
===Module Description===
This module converts Diffusion weighted MR images in Dicom format into
+
This module converts diffusion weighted MR images in dicom series into Nrrd
NRRD format. The module assumes that the reference space for dicom is
+
format for analysis in Slicer. This program has been tested on only
always RAS. Currently, the module supports GE format, Simens mosaic and
+
a limited subset of DTI dicom formats available from Siemens, GE,
split formats, and Philips format.
+
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.
  
 
== Usage ==
 
== Usage ==
 +
 +
When this module is run from Slicer UI, simply select the "DICOM Directory" and "Output Image Volume" and press "Apply" button.
 +
 +
The module can also be run from command line to enable batch process. An example command line look like:
 +
 +
d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
 +
 
<pre>
 
<pre>
 
./DicomToNrrdConverter --help
 
./DicomToNrrdConverter --help
Line 30: Line 46:
 
                                         [--processinformationaddress
 
                                         [--processinformationaddress
 
                                         <std::string>] [--xml] [--echo]
 
                                         <std::string>] [--xml] [--echo]
                                         [--] [--version] [-h] <std::string>
+
                                         [--useIdentityMeaseurementFrame]
                                         <std::string>
+
                                        [--writeProtocolGradientsFile]
 
+
                                        [--useLPS] [--outputVolume
 +
                                        <std::string>]
 +
                                        [--inputDicomDirectory
 +
                                         <std::string>] [--] [--version]
 +
                                        [-h]
  
 
Where:
 
Where:
Line 45: Line 65:
 
   --echo
 
   --echo
 
     Echo the command line arguments (default: 0)
 
     Echo the command line arguments (default: 0)
 +
 +
  --useIdentityMeaseurementFrame (advanced option, use default)
 +
    Adjust all the gradients so that the measurement frame is an identity
 +
    matrix. (default: 0)
 +
 +
  --writeProtocolGradientsFile (advanced option, for debug)
 +
    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. (default: 0)
 +
 +
  --useLPS (advanced option, use default)
 +
    For GE data only.  Specifies that the output should be in LPS space
 +
    like the original DICOM data.  The default is to use Slicer3
 +
    consistent RAS space. (default: 0)
 +
 +
  --outputVolume <std::string>
 +
    Output Image in NRRD format (.nhdr)
 +
 +
  --inputDicomDirectory <std::string>
 +
    Directory holding Dicom series
  
 
   --,  --ignore_rest
 
   --,  --ignore_rest
Line 55: Line 97:
 
     Displays usage information and exits.
 
     Displays usage information and exits.
  
  <std::string>
+
   Description: Converts diffusion weighted MR images in dicom series into Nrrd
    (required)  Directory holding Dicom series
+
   format for analysis in Slicer. This program has been tested on only
 
+
  a limited subset of DTI dicom formats available from Siemens, GE,
  <std::string>
+
  and Phillips scanners. Work in progress to support dicom multi-frame
    (required)  Nrrd header file name
+
  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.  
   Description: Converts diffusion weighted MR images in dicom series into
 
   Nrrd format.
 
  
 
   Author(s): Xiaodong Tao
 
   Author(s): Xiaodong Tao
Line 70: Line 110:
 
   Image Computing (NAMIC), funded by the National Institutes of Health
 
   Image Computing (NAMIC), funded by the National Institutes of Health
 
   through the NIH Roadmap for Medical Research, Grant U54 EB005149.
 
   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.
 
</pre>
 
</pre>

Latest revision as of 19:47, 25 November 2009

Home < Modules:DicomToNRRD-3.4

Return to Slicer 3.4 Documentation

Gallery of New Features

Module Name

DWI Dicom To NRRD

General Information

Module Type & Category

Type: Command line module

Category: Converters

Screenshot of the UI

Authors, Collaborators & Contact

  • Author: Xiaodong Tao (with contribution from Vince Magnotta and Hans Johnson)
  • Contact: taox @ research.ge.com

Module Description

This module 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.

Usage

When this module is run from Slicer UI, simply select the "DICOM Directory" and "Output Image Volume" and press "Apply" button.

The module can also be run from command line to enable batch process. An example command line look like:

d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr

./DicomToNrrdConverter --help

USAGE:

   d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe
                                        [--processinformationaddress
                                        <std::string>] [--xml] [--echo]
                                        [--useIdentityMeaseurementFrame]
                                        [--writeProtocolGradientsFile]
                                        [--useLPS] [--outputVolume
                                        <std::string>]
                                        [--inputDicomDirectory
                                        <std::string>] [--] [--version]
                                        [-h]

Where:

   --processinformationaddress <std::string>
     Address of a structure to store process information (progress, abort,
     etc.). (default: 0)

   --xml
     Produce xml description of command line arguments (default: 0)

   --echo
     Echo the command line arguments (default: 0)

   --useIdentityMeaseurementFrame (advanced option, use default)
     Adjust all the gradients so that the measurement frame is an identity
     matrix. (default: 0)

   --writeProtocolGradientsFile (advanced option, for debug)
     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. (default: 0)

   --useLPS (advanced option, use default)
     For GE data only.  Specifies that the output should be in LPS space
     like the original DICOM data.  The default is to use Slicer3
     consistent RAS space. (default: 0)

   --outputVolume <std::string>
     Output Image in NRRD format (.nhdr)

   --inputDicomDirectory <std::string>
     Directory holding Dicom series

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   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. 

   Author(s): 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.