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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

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

Gordon Kindlmann

Laboratory for Mathematics in Imaging

outline
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
dwi crash course mri
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
dwi crash course model
DWI crash course: Model

Single Tensor Model (Basser 1994)

Ai

Dxz

Dxx

Dxy

Tensor

estimation

D

A0

Dyy

Dyz

Dzz

gi

dwi crash course math
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
dwi crash course coordinates

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”

nrrd dwi headers motivation
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
nrrd dwi header status
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

nrrd dwi header generation
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 -

nrrd dwi header support
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.

nrrd dwi header data file possibilities
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

deft interactive tensor vis
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
deft pointers
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