1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org A DW-MRI processing and visualization pipeline for NA-MIC Gordon Kindlmann Laboratory for Mathematics in Imaging

2. National Alliance for Medical Image Computing http://na-mic.org Outline Crash course on DWI and DTI –The necessity of 3 coordinate frames NRRD DWI headers –Motivation, creation, inspection Command-line Teem tools –“unu” + “tend” for pre-processing –relationship to other software (ITK) Deft: new interactive DTI visualization –Intro to underlying Teem API

3. National Alliance for Medical Image Computing http://na-mic.org DWI crash course: MRI Diffusion: Brownian motion of one material through another Anisotropy: diffusion rate depends on direction Magnetic gradients create spatial planar waves of proton phase Destructive interference measures diffusion along gradient direction only Kleenex newspaper

4. National Alliance for Medical Image Computing http://na-mic.org DWI crash course: Model Single Tensor Model (Basser 1994) A0A0 gigi AiAi D Dxx Dxy Dxz Dyy Dyz Dzz Tensor estimation

5. National Alliance for Medical Image Computing http://na-mic.org DWI crash course: Math Knowns: b, g i (or B i ) Measured: A 0, A i Find: D Most common: linear least squares on Better: non-linear least squares

6. National Alliance for Medical Image Computing http://na-mic.org DWI crash course: Coordinates right anterior superior World: e.g. “RAS” fast=I medium=J slow=K Image: “IJK” Gradients: g 1 = (1,0,1) g 2 = (1,-1,0) …  D xx, D xy … x y z “Image Orientation” “Measurement Frame”

7. National Alliance for Medical Image Computing http://na-mic.org NRRD DWI headers : Motivation File format need –Self-contained representation –All image values (in original files) –All DWI-specific parameters (b, g i, etc.) –All coordinates (including measurement frame!!) –DICOM is not a solution (DWI or DTI) Manual sign flips/transposition  Store answer NA-MIC solution: –NRRD format + key/value pair convention –NRRD: image values + coordinates Explicit representation of measurement frame –Key/value pair convention: DWI-specific parameters

8. National Alliance for Medical Image Computing http://na-mic.org NRRD DWI header: Status See updated info on Wiki http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format Changes from last SLC AHM (~year ago) –“measurement frame”: NRRD0004 to NRRD0005 –Key/value pair convention was broken, now fixed modality:=DW modality:=DWMRI DW_gradient_001:= 1 0 0 DWMRI_b-value:=800 DWMRI_gradient_0001:= 1 0 0 –BWH (“HUVA…”) DWI data on BIRN needs new headers from separate tarball, also on BIRN Command-tool (unu/tend) usage examples: http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples

9. National Alliance for Medical Image Computing http://na-mic.org NRRD DWI header: Generation Written by: hand? –Automated extraction from DICOM (for all possible scanners) simply impossible at this point. –Would be very nice to have a DWI “wizard” –“unu make” is good for make sure individual data files can be read in with “-bs -1” trick unu make -i S4.130 -s 256 256 -t short \ -e raw -en little -bs -1 \ | unu quantize -b 8 | unu save -f pnm | xv - (“pv” on windows- bug me later) unu make -i S4.1?? -s 256 256 100 -t short\ -e raw -en little -bs -1 \ | unu tile -a 2 0 1 -s 10 10 \ | unu quantize -b 8 | unu save -f pnm | xv -

10. National Alliance for Medical Image Computing http://na-mic.org NRRD DWI header: Support Read by Teem/NrrdIO Slicer (can read both DWI and DTI) –See Wiki for instructions ITK (both DWI and DTI) –See Wiki for instructions - Insight/Code/IO/itkNrrdImageIO.cxx handles mapping between NRRD’s N+1 logical array dimension (one axis for multi-values) to N- dimensional image.

11. National Alliance for Medical Image Computing http://na-mic.org NRRD DWI header: data file possibilities Volume interleaved, volume at a time: data file: dwi%03d.gipl 1 12 1 byte skip: -1 sizes: 256 256 60 12 kinds: space space space list Volume interleaved: slice at a time data file: MR_0028_%04d.dcm 1 448 1 2 byte skip: -1 sizes: 128 128 64 7 kinds: space space space list Slice interleaved: slice at a time data file: test_%04d.dcm 1 448 1 2 byte skip: -1 sizes: 128 128 7 64 kinds: space space list space

12. National Alliance for Medical Image Computing http://na-mic.org Deft: interactive tensor vis Deft: written in C++/OpenGL –Built on top of Teem (written in C) –Compiled with Cmake MIT License –Teem is LGPL+static linking exceptions Deft is not for clinicians –low-level data inspection: “xv for tensors” (glyphs) –Algorithmic visualization: exploring parameters (fibers) –Possible example of light-weight stand-alone Slicer3 data client Benchmarking for visualization speed (glyphs) Comparison/”Validation” with different tractography method

13. National Alliance for Medical Image Computing http://na-mic.org Deft pointers Start with Deft::Viewer “Camera Reset” button Camera control: cursor location determines effect 2D Rotate Vertical axis rotate Horz axis rotate Field of View In-screen-plane rotate Dolly Translate Horz Translate Vert Translate Field of View Translate along view dir Depth of near/far clipping planes Left-clickRight-click (Mac: cmd-click)