1. Surgical Planning Laboratory http://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.

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Women’s Hospital Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 Laboratory of Mathematics in Imaging, Brigham and Women’s Hospital Thanks to Gordon Kindlmann

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Women’s Hospital Goal of the Tutorial Training on how to generate NRRD headers DTI data and validate the orientation information within Slicer.

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Women’s Hospital Which image is correct ?

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Women’s Hospital The right one is correct

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Women’s Hospital 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

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Women’s Hospital 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

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Women’s Hospital Nearly Raw Raster Data Image files that include a NRRD header to accurately represent N-dimensional raster data 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: the software provides you a visual tool to confirm that the orientation of the tensors is consistent with expected neuroanatomy

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Women’s Hospital DTI Pipeline DWI images Diffusion Sensitizing Gradients Dxx Dxy Dxz Dyy Dyz Dzz DTI images

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Women’s Hospital Coordinate frames DWI and DTI Image Orientation (I,J,K) Diffusion Sensitizing Gradients (X,Y,Z) (I,J,K) Patient Space (R,A,S)

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Women’s Hospital Transformation matrices (X,Y,Z) (I,J,K) (R,A,S) T: XYZ  RAST: IJK  RAS

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Women’s Hospital NRRD Terminology (X,Y,Z)(I,J,K) (R,A,S) T: XYZ  RAS T: IJK  RAS

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Women’s Hospital 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

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Women’s Hospital 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

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Women’s Hospital 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

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Women’s Hospital 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 NRRD reader to load DTI volumes in Nrrd format

17. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Women’s Hospital Unu syntax General Syntax: unu cmd -i input -o output Tips: “unu”  list of unu commands “unu cmd”  help on cmd

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Women’s Hospital Unu syntax: ‘make’ command ‘make’ syntax: unu make -i input -o output ‘make’ documentation: unu make  help on make

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Women’s Hospital 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

20. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Women’s Hospital 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

21. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Women’s Hospital 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)"

22. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Women’s Hospital Complete unu Command 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

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Women’s Hospital 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

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Women’s Hospital Step1: Unu Command into Slicer Type the unu command directly in the Tk console of Slicer

25. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Women’s Hospital Step 2: Adding axis description You need to add an additionnal 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)

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Women’s Hospital Step 2: Adding axis description Type the following Tcl commands: set file [open myTensors.nhdr a] puts $file “kinds: space space space 3d-symmetric-matrix” close $file

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Women’s Hospital Step 2: Axis description In this example kinds states that the data is stored with the tensors coefficients in the slowest axis.

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Women’s Hospital Step 3: Viewing the NRRD Header Type more MyNrrdFile.nhdr in the Tk console to display the content of the NRRD header you just made

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Women’s Hospital Step 3: Viewing the Nrrd Header Slicer displays the content of the Nrrd header

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Women’s Hospital 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

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Women’s Hospital Loading a NRRD Volume Click on Add Volume in the Main Panel of Slicer

32. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Women’s Hospital Loading a NRRD Volume Select Nrrd Reader in the Properties field Click on Browse and load the file myTensors.nhdr Click on Apply The Props Panel of the module Volumes appears.

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Women’s Hospital Loading a NRRD Volume Slicer loads the Nrrd Tensor

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Women’s Hospital Fractional Anisotropy Compute the Fractional Anisotropy from the Nrrd Tensor Volume using the DT-MRI module (Slicer Training 4)

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Women’s Hospital Corpus Callosum Tracts Seed tracts in the Corpus Callosum using the tractography tools from the DT-MRI module (Slicer Training 4)

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Women’s Hospital Corpus Callosum Tracts The orientation of the tracts within the Corpus Callosum confirms that the orientation information contained in the Nrrd file is correct.

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Women’s Hospital The right one is correct

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Women’s Hospital Conclusion Standardized description of the information contained in DWI and DTI data. Rapid, intuitive visual assessment of orientation results within Slicer Open-Source: http://teem.sourceforge.net/nrrd/