surgical planning laboratory -1- brigham and womens hospital converting dti data into nrrd file...
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Surgical Planning Laboratoryhttp://www.slicer.org-1-
Brigham and Women’s Hospital
Converting DTI data into Nrrd file format
Sonia Pujol, Ph.D.
Gordon Kindlmann, Ph.D.
Randy Gollub, M.D, Ph.D.
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Acknowledgments
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
Section on Tissue Biophysics and BiomimeticsNational Institutes of HealthThanks to Dr. Carlo Pierpaoli
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Disclaimer
It is the responsibility of the user of 3DSlicer
to comply with both the terms of the license
and with the applicable laws, regulations
and rules.
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Material
• Slicer 2.6http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started
• Tensor Sample Data Set Tensor_data.ziphttp://www.na-mic.org/Wiki/index.php/Slicer:Workshop:User_Training_101
• PrerequisitesThis tutorial assumes that you have already completed
– Slicer Basics Loading and Viewing Data (Slicer Training 1)– Slicer DT-MRI ( Slicer Training 8)
http://www.na-mic.org/Wiki/index.php/Slicer:Workshop:User_Training_101
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Goal of the Tutorial
Training on how to generate Nrrd headers DTI data and validate the orientation information within Slicer.
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Which image is correct ?
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Which image is correct ?
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The right one is correct
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Overview
• Part 1: Nrrd description• Part 2: Nrrd requirements • Part 3: Generating Nrrd Files• Part 4: Nrrd training data• Part 5: Orientation validation within Slicer
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Background• Challenge: Concise and standardized description of
the information contained in DWI and DTI data.• Current situation:
– DICOM (Supplement 49) contains information on how to represent b-values and gradient directions of DWI
– However no-one uses it: every vendor has their own unique way of archiving the relevant image acquisition parameters
– The definition of the coordinate frame of the diffusion gradients (or the resulting estimated tensor) is not explicitly recorded in the header.
– DICOM has no standard for tensors
• Proposed Solution: Nrrd format
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Nearly Raw Raster Data (Nrrd)• The flexible Nrrd format includes a single header file
and image file(s) that can be separate or combined.
• A Nrrd header accurately represents N-dimensional raster information for scientific visualization and medical image processing.
• NA-MIC has developed a way of using the Nrrd format to represent Diffusion Weighted Images (DWI) volumes and Diffusion Tensor Images (DTI).
• Nrrd DWI and Nrrd DTI data can be read into 3D Slicer, to visually confirm that the orientation of the tensors is consistent with expected neuroanatomy
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DTI Pipeline
DWI imagesDiffusion Sensitizing Gradients
Dxx Dxy Dxz
Dyy Dyz
Dzz
DTI images
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Coordinate frames
DWI and DTI Image Orientation
(I,J,K)
Diffusion Sensitizing Gradients
(X,Y,Z) (X,Y,Z) (I,J,K)
Patient Space
(R,A,S)
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Transformation matrices
T: IJKRAS
(X,Y,Z) (I,J,K)
T: XYZRAS
(R,A,S)
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Nrrd Terminology
T: XYZRAS
(X,Y,Z) (I,J,K)
(R,A,S)
T: IJKRAS
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Overview
• Part 1: Nrrd description• Part 2: Nrrd requirements • Part 3: Generating Nrrd Files• Part 4: Nrrd training data• Part 5: Orientation validation within Slicer
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DTI RequirementsTo generate a Nrrd header for DTI data, you’ll need to know
about the data representation and acquisition:
DTI Volume characteristics• Data Type • Endianess• Dimensions
Disk Storage• Axis Ordering
Coordinate Frames• DTI Image Orientation• Gradient Measurement Frame
Tensor coefficients• Order of the tensor coefficients
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Overview
• Part 1: Nrrd description• Part 2: Nrrd requirements • Part 3: Generating Nrrd Files• Part 4: Nrrd training data• Part 5: Orientation validation within Slicer
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Generating Nrrd Files
• Nrrd files can be generated from the Tk console of Slicer using the “unu” command line tool
• unu is part of set of libraries called “Teem” compiled into Slicer 2.6
(http://teem.sourceforge.net/)• Slicer includes a Nrrd reader to load DTI volumes in Nrrd
format
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Unu syntax
• General Syntax:
unu cmd -i input -o output
• Tips:
“unu” list of unu commands
“unu cmd” help on cmd
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Unu syntax: ‘make’ command
• ‘make’ syntax:
unu make -i input -o output
• ‘make’ documentation:
unu make help on make
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Running unu on Mac/Linux/Solaris To run the unu command from the Tk console, type ./unu• on Mac, you need to be in the directory
/Lib/darwin-ppc/teem-build/bin• on Linux, you need to be in the directory
/Lib/linux-x86/teem-build/bin• on Solaris, you need to be in the directory
/Lib/solaris8/teem-build/bin.
Another option for Mac/Linux/Solaris platforms is to
enter the whole path to the /bin directory containing
the executables when running the command.
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Running unu on Windows
To run the unu command from the Tk
console, type unu.
On Windows, you do not need to be in the
directory win32/bin/teem-build: the unu
commands run from any location.
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Overview
• Part 1: Nrrd description• Part 2: Nrrd requirements • Part 3: Generating Nrrd Files• Part 4: Nrrd DTI training data• Part 5: Orientation validation within Slicer
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Creating Nrrd header for the DTIDTI Training Data
From the Analyze header, extract the:
• DTI Volume characteristicsData Type: Float “--type float”Endianess: Big Endian “--endian big”Dimensions: 91 109 91 6 “--size 91 109 91 6”
• Disk StorageAxis Ordering: columns, rows, slices, tensor elements “--kinds space space space 3d-symmetric-matrix”
• Tensor coefficientsOrder of the tensor coefficients: Dxx, Dyy, Dzz, Dxy,Dxz, Dyz
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DTI Training Data• Coordinate FramesDTI Image Orientation: Right-Anterior-Superior “--space ras”
• Tensors Measurement FrameT: XYZRAS “--measurement frame (1,0,0) (0,1,0) (0,0,1)”
• Space Direction and SpaceOrigin
T: IJKRAS --directions "(-1.98901,0.0,0.0) (0.0,1.99083,0.0)
(0.0,0.0,2.0) --origin "(0,0,0)"
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Complete unu Command (Mac/Linux/Solaris)
./unu make -h -i Tensors.img --size 91 109 91 6 --type float --encoding raw --endian big --space ras --spaceunit mm mm mm --measurementframe "(1,0,0)(0,1,0)(0,0,1)“ --directions "(-1.98901,0.0,0.0) (0.0,1.99083,0.0) (0.0,0.0,2.0) none" --origin "(0,0,0)" | unu shuffle -a 3 -p 0 3 4 1 5 2 -o myTensors.nhdr
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Complete unu Command (Windows)
unu make -h -i Tensors.img --size 91 109 91 6 --type float --encoding raw --endian big --space ras --spaceunit mm mm mm --measurementframe "(1,0,0)(0,1,0)(0,0,1)“ --directions "(-1.98901,0.0,0.0) (0.0,1.99083,0.0) (0.0,0.0,2.0) none" --origin "(0,0,0)" | unu shuffle -a 3 -p 0 3 4 1 5 2 -o myTensors.nhdr
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Reordering the Tensor Coefficients
Initial tutorial dataset 0:Dxx 1:Dyy 2:Dzz 3:Dxy 4:Dxz 5:Dyz
Final tutorial dataset 0:Dxx 3:Dxy 4:Dxz 1:Dyy 5:Dyz 2:Dzz
unu shuffle –a 3 –p 0 3 4 1 5 2
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Step1: Unu Command into Slicer
Type the unu command directly in the Tk console of Slicer
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Step 2: Adding axis description
You need to add an additional kinds field to the generated Nrrd header to specify how the data is stored to disk
(This is analogous to the “Intent” field in NIfTI file format)
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Step 2: Adding axis descriptionType the following Tcl commands in the Tk console:
set file [open myTensors.nhdr a]
puts $file “kinds: space space space 3d-symmetric-matrix”
close $file
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Step 2: Axis description
In this example kinds states that the data is stored with the tensors coefficients in the slowest axis.
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Step 3: Viewing the NRRD Header
Type more MyTensors.nhdr in the Tk console to display the content of the NRRD header you just made
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Step 3: Viewing the Nrrd Header
Slicer displays the content of the Nrrd header
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Overview
• Part 1: Nrrd description• Part 2: Nrrd requirements • Part 3: Generating Nrrd Files• Part 4: Nrrd training data• Part 5: Orientation validation within Slicer
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Loading a Nrrd Volume
Click on Add Volume in the Main Panel of Slicer
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Loading a Nrrd Volume
Select Nrrd Reader in the Properties field
Click on Browse and load the file myTensors.nhdr
The Props Panel of the module Volumes appears.
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Loading a Nrrd Volume
Click on Apply
Check that the path to myTensors.nhdr is correctly loaded.
If needed, type the correct path directly in the window.
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Loading a Nrrd Volume
Slicer loads the Nrrd Tensor
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Fractional Anisotropy
Compute the Fractional Anisotropy from the Nrrd Tensor Volume using the DT-MRI module
(Slicer Training 4)
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Corpus Callosum Tracts
Seed tracts in the Corpus Callosum using the tractography tools from the DT-MRI module
(Slicer Training 4)
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Corpus Callosum Tracts
The orientation of the tracts within the Corpus Callosum confirms that the orientation information contained in the Nrrd file is correct.
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The right one is correct
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Conclusion
• Standardized description of the information contained in DTI data.
• Rapid, intuitive visual assessment of orientation results within Slicer
• Open-Source: http://teem.sourceforge.net/nrrd/