DICOM to NRRD Conversion Tutorial
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DICOM to NRRD Conversion Tutorial
Martin Styner
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University of North CarolinaNeuro Image Research and Analysis Lab
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DICOM to NRRD Tutorial
This tutorial guides you through the process of converting DICOM files from a DWI acquisition into a NRRD volume, load that DWI volume into 3D Slicer for further processing.
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Dataset
For this tutorial you will need some DICOM data files that can be found on this link :http://hdl.handle.net/1926/1759
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Start Slicer 4
Linux/Mac users :Launch the Slicerexecutable located inthe Slicer4 directory
Windows users :Select StartAll ProgramsSlicer4.2.1.1SlicerOr launch the Slicer executable from Slicer4 directory 4
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Welcome Module
The Slicer Welcome module is the module displayed by default. This module gives an overview of the GUI of Slicer4, and data loading & saving functionality.
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DICOMtoNRRD Module
Left click on the menu Modules and select All Modules to display the list of modules available for image analysis and 3D visualization.Select the module Dicom to Nrrd converter 6
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DICOMtoNRRD Module
Select the Input DICOM directorySelect the Output directoryChoose an Output name for your Nrrd file
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DICOMtoNRRD Module
Left click on Output Option to get it extendedLeft click on the 3rd check box (Use Bmatrix Gradient Directions)Left click on Apply button
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What does Bmatrix Box do?
• Uses B-matrix to compute the diffusion gradient information– B-Matrix is the actual diffusion matrix applied
during acquisition– Principal eigenvector of B-Matrix is the diffusion
gradient direction• Potential for incorrect/inadequate information
in the diffusion gradient direction– B-Matrix use is safest, if present– Siemens DICOM provide B-Matrix information
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Loading DWI NRRD Volume
Click on Data icon
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Choose File to Add
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Select Choose Files to Add
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Choose File to Add
Select your previously created Nrrd volume
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Choose File to Add
Select “OK”
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Volumes
Left click on the volume icon
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Volumes
Select volume you just opened in “Active Volume” SectionAdjust viewed DWI Component
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Conclusion
This tutorial guided you through the conversion from DICOM to NRRD file using Slicer 4 Software
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Acknowledgment
• National Alliance for Medical Image ComputingNIH U54EB005149
• Contributors: Jean-Baptiste Berger, Clement Vachet, Zhexing Liu, Guido Gerig, Sylvain Gouttard