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A DW-MRI processing and visualization pipeline for NA-MIC

A DW-MRI processing and visualization pipeline for NA-MIC. Gordon Kindlmann Laboratory for Mathematics in Imaging. Outline. Crash course on DWI and DTI The necessity of 3 coordinate frames NRRD DWI headers Motivation, creation, inspection Command-line Teem tools

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A DW-MRI processing and visualization pipeline for NA-MIC

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  1. A DW-MRI processing and visualization pipeline for NA-MIC Gordon Kindlmann Laboratory for Mathematics in Imaging

  2. 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. DWI crash course: MRI newspaper Kleenex • 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

  4. DWI crash course: Model Single Tensor Model (Basser 1994) Ai Dxz Dxx Dxy Tensor estimation D A0 Dyy Dyz Dzz gi

  5. DWI crash course: Math • Knowns: b, gi (or Bi) • Measured: A0, Ai • Find: D • Most common: linear least squares on • Better: non-linear least squares

  6. Image: “IJK” x Gradients: g1 = (1,0,1) g2 = (1,-1,0) … Dxx, Dxy … slow=K y medium=J z fast=I World: e.g. “RAS” superior anterior right DWI crash course: Coordinates “Image Orientation” “Measurement Frame”

  7. NRRD DWI headers : Motivation • File format need • Self-contained representation • All image values (in original files) • All DWI-specific parameters (b, gi, 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. 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. 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. 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. 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. 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. Deft pointers • Start with Deft::Viewer “Camera Reset” button • Camera control: cursor location determines effect Left-click Right-click (Mac: cmd-click) Horz Translate Vertical axis rotate Translate 2D Rotate Horz axis rotate Vert Translate Field of View Field of View Translate along view dir In-screen-plane rotate Depth of near/far clipping planes Dolly

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