Converting DTI data into Nrrd file format

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.



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



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.



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



Goal of the Tutorial

Training on how to generate Nrrd headers DTI data and validate the orientation information within Slicer.



Which image is correct ?



Which image is correct ?



The right one is correct



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



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



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



DTI Pipeline

DWI imagesDiffusion Sensitizing Gradients

Dxx Dxy Dxz

Dyy Dyz

Dzz

DTI images



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)



Transformation matrices

T: IJKRAS

(X,Y,Z) (I,J,K)

T: XYZRAS

(R,A,S)



Nrrd Terminology

T: XYZRAS

(X,Y,Z) (I,J,K)

(R,A,S)

T: IJKRAS



Overview




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



Overview




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



Unu syntax

• General Syntax:

unu cmd -i input -o output

• Tips:

“unu” list of unu commands

“unu cmd” help on cmd



Unu syntax: ‘make’ command

• ‘make’ syntax:

unu make -i input -o output

• ‘make’ documentation:

unu make help on make



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.



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.



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



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



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)"



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



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



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



Step1: Unu Command into Slicer

Type the unu command directly in the Tk console of Slicer



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)



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



Step 2: Axis description

In this example kinds states that the data is stored with the tensors coefficients in the slowest axis.



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



Step 3: Viewing the Nrrd Header

Slicer displays the content of the Nrrd header



Overview




Loading a Nrrd Volume

Click on Add Volume in the Main Panel of Slicer




Select Nrrd Reader in the Properties field

Click on Browse and load the file myTensors.nhdr

The Props Panel of the module Volumes appears.




Click on Apply

Check that the path to myTensors.nhdr is correctly loaded.

If needed, type the correct path directly in the window.




Slicer loads the Nrrd Tensor



Fractional Anisotropy

Compute the Fractional Anisotropy from the Nrrd Tensor Volume using the DT-MRI module

(Slicer Training 4)



Corpus Callosum Tracts

Seed tracts in the Corpus Callosum using the tractography tools from the DT-MRI module

(Slicer Training 4)



Corpus Callosum Tracts

The orientation of the tracts within the Corpus Callosum confirms that the orientation information contained in the Nrrd file is correct.



The right one is correct



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/

Documents

Converting DTI data into Nrrd file format