1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Womens 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 Womens Hospital 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

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Womens Hospital 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.

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Womens Hospital 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

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Womens Hospital Goal of the Tutorial Training on how to generate Nrrd headers DTI data and validate the orientation information within Slicer.

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Womens Hospital Which image is correct ?

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Womens Hospital Which image is correct ?

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Womens Hospital The right one is correct

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Womens 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

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Womens 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

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Womens Hospital 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

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Womens Hospital DTI Pipeline DWI images Diffusion Sensitizing Gradients Dxx Dxy Dxz Dyy Dyz Dzz DTI images

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Womens 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)

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Womens Hospital Transformation matrices T: IJK RAS (X,Y,Z) (I,J,K) T: XYZ RAS (R,A,S)

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Womens Hospital Nrrd Terminology T: XYZ RAS (X,Y,Z)(I,J,K) (R,A,S) T: IJK RAS

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Womens 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

17. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Womens Hospital DTI Requirements To generate a Nrrd header for DTI data, youll 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

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Womens 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

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Womens 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 a Nrrd reader to load DTI volumes in Nrrd format

20. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Womens Hospital Unu syntax General Syntax: unu cmd -i input -o output Tips: unu list of unu commands unu cmd help on cmd

21. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Womens Hospital Unu syntax: make command make syntax: unu make -i input -o output make documentation: unu make help on make

22. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Womens Hospital 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.

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Womens Hospital 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.

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Womens Hospital 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

25. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Womens Hospital DTI 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

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Womens 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)"

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Womens Hospital 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

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Womens Hospital 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

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Womens 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

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Womens Hospital Step1: Unu Command into Slicer Type the unu command directly in the Tk console of Slicer

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Womens Hospital 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)

32. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Womens Hospital 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 3d- symmetric-matrix close $file

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Womens Hospital Step 2: Axis description In this example kinds states that the data is stored with the tensors coefficients in the slowest axis.

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Womens Hospital 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

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Womens Hospital Step 3: Viewing the Nrrd Header Slicer displays the content of the Nrrd header

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Womens 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

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Womens Hospital Loading a Nrrd Volume Click on Add Volume in the Main Panel of Slicer

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Womens Hospital 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.

39. Surgical Planning Laboratory http://www.slicer.org -39- Brigham and Womens Hospital 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.

40. Surgical Planning Laboratory http://www.slicer.org -40- Brigham and Womens Hospital Loading a Nrrd Volume Slicer loads the Nrrd Tensor

41. Surgical Planning Laboratory http://www.slicer.org -41- Brigham and Womens Hospital Fractional Anisotropy Compute the Fractional Anisotropy from the Nrrd Tensor Volume using the DT-MRI module (Slicer Training 4)

42. Surgical Planning Laboratory http://www.slicer.org -42- Brigham and Womens Hospital Corpus Callosum Tracts Seed tracts in the Corpus Callosum using the tractography tools from the DT-MRI module (Slicer Training 4)

43. Surgical Planning Laboratory http://www.slicer.org -43- Brigham and Womens 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.

44. Surgical Planning Laboratory http://www.slicer.org -44- Brigham and Womens Hospital The right one is correct

45. Surgical Planning Laboratory http://www.slicer.org -45- Brigham and Womens Hospital 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/