Transcript Converting DTI data into Nrrd file format Sonia Pujol, Ph.D. Gordon Kindlmann, Ph.D. Randy Gollub, M.D, Ph.D. Surgical Planning Laboratory -1- http://www.slicer.org 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.
Surgical Planning Laboratory
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Acknowledgments
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218
Section on Tissue Biophysics and Biomimetics
National Institutes of Health
Thanks 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 2.6
http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started
• Tensor Sample Data Set
Tensor_data.zip
http://www.na-mic.org/Wiki/index.php/Slicer:Workshop:User_Training_101
• Prerequisites
This 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
Dxx Dxy Dxz
Dyy Dyz
Dzz
Diffusion
Sensitizing
Gradients
DWI images
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DTI images
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Coordinate frames
Diffusion
Sensitizing
Gradients
DWI and DTI
Image
Orientation
(X,Y,Z)
(X,Y,Z)
(I,J,K)
(I,J,K)
Patient Space
(R,A,S)
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Transformation matrices
(I,J,K)
(X,Y,Z)
T: XYZRAS
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T: IJKRAS
(R,A,S)
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Nrrd Terminology
(X,Y,Z)
(I,J,K)
T: XYZRAS
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T: IJKRAS
(R,A,S)
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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 Requirements
To 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 DTI Training Data
From the Analyze header, extract the:
• DTI Volume characteristics
Data Type: Float  “--type float”
Endianess: Big Endian  “--endian big”
Dimensions: 91 109 91 6  “--size 91 109 91 6”
• Disk Storage
Axis Ordering: columns, rows, slices,
tensor elements
 “--kinds space space space 3d-symmetric-matrix”
• Tensor coefficients
Order of the tensor coefficients: Dxx, Dyy, Dzz, Dxy,Dxz, Dyz
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DTI Training Data
• Coordinate Frames
DTI Image Orientation:
Right-Anterior-Superior
 “--space ras”
• Tensors Measurement Frame
T: XYZRAS
“--measurement frame (1,0,0) (0,1,0) (0,0,1)”
• Space Direction and SpaceOrigin
T: IJKRAS
 --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
unu shuffle –a 3 –p 0 3 4 1 5 2
Final tutorial dataset
0:Dxx 3:Dxy 4:Dxz 1:Dyy 5:Dyz 2:Dzz
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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 description
Type the following Tcl commands in the Tk
console:
set file [open myTensors.nhdr a]
puts $file “kinds: space space space 3dsymmetric-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
The Props Panel of the module
Volumes appears.
Select Nrrd Reader in
the Properties field
Click on Browse and load the
file myTensors.nhdr
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Loading a Nrrd Volume
Check that the path to
myTensors.nhdr is
correctly loaded.
If needed, type the correct
path directly in the window.
Click on
Apply
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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/
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