NA-MICNational Alliance for Medical Image Computing http://na-mic.org

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

Gordon KindlmannLaboratory for Mathematics in Imaging

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

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

National Alliance for Medical Image Computing http://na-mic.org

DWI crash course: Model

Single Tensor Model (Basser 1994)

A0

gi

Ai

D

Dxx Dxy Dxz

Dyy Dyz

Dzz

Tensorestimation

National Alliance for Medical Image Computing http://na-mic.org

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

National Alliance for Medical Image Computing http://na-mic.org

DWI crash course: Coordinates

rightanterior

supe

riorWorld:

e.g. “RAS”

fast=I

med

ium

=J

slow=KImage:“IJK” Gradients:

g1 = (1,0,1)g2 = (1,-1,0)… Dxx, Dxy …

x

y

z

“ImageOrientation”

“MeasurementFrame”

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, 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

National Alliance for Medical Image Computing http://na-mic.org

NRRD DWI header: Status

• See updated info on Wikihttp://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

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 -

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.

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 1byte skip: -1sizes: 256 256 60 12kinds: space space space list

Volume interleaved: slice at a timedata file: MR_0028_%04d.dcm 1 448 1 2byte skip: -1sizes: 128 128 64 7kinds: space space space list

Slice interleaved: slice at a timedata file: test_%04d.dcm 1 448 1 2byte skip: -1sizes: 128 128 7 64kinds: space space list space

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

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

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rota

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Fie

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f Vie

w

In-screen-plane rotate

Dolly

Translate

Horz Translate

Ve

rt T

rans

late

Fie

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f Vie

w

Translate along view dir

Depth of near/far clipping planes

Left-click Right-click (Mac: cmd-click)