MeningiomaMRIRegistrationStudy

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Objective

Accurate registration of same patient/same modality MRI data for longitudinal analysis of tumor progression.

Specific Aims

  1. Compare the accuracy of registration using existing Slicer and non-Slicer tools
  2. Identify parameter settings that produce satisfactory results
  3. Outline the limitations of the available registration tools in the context of the specific clinical research application

Data

  • Input images: isotropic post-contrast T1 MRI acquired at different locations of BWH during 2006-2008, used under medical records study IRB. Time period between acquisition of scans for each patient is about 1 year.
  • Ground truth transformation: not available
  • Expert landmarks for registration evaluation: not available
  • Checkerboard appearance of unregistered images for the representative data of interest
    • Case01
    • Case03
    • Case04
    • Case10

Environment

All registration methods were executed on george.bwh.harvard.edu. Where number of threads was possible to specify, it was set to 4.

Measures of success

  • qualitative assessment: visually pleasing results
  • quantitative assessment: something better than "visually pleasing" (TBD)
  • minimum execution time to meet the application requirements: interactive quantification of tumor growth

Methods

Registration

RegisterImages Slicer module

RigidRegistration Slicer module

BRAINSFit

${SLICER} --launch BRAINSFitExe \
  --fixedVolume ${TIME_POINT_1}  --movingVolume ${TIME_POINT_2} \
  --transformType Rigid --initializeTransformMode CenterOfHead \
  --numberOfIterations 200 --numberOfSamples 100000 --minimumStepSize 0.005 \
  --spatialScale 1000 --reproportionScale 1 \
  --outputTransform ${BF_TRANSFORM} --histogramMatch \
  --strippedOutputTransform ${BF_STRIPPED_TRANSFORM} \
  --patientID ANON --studyID ANON --outputVolumePixelType float \
  --backgroundFillValue 0 --maskProcessingMode ROIAUTO \
  --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 \
  --fixedVolumeOrigin 0,0,0 --movingVolumeOrigin 0,0,0 \
  --medianFilterSize 0,0,0 --permitParameterVariation 1,1,1 \
  --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode Whatever \
  --relaxationFactor 0.5 --maximumStepSize 0.2 --failureExitCode -1 \
  --fixedVolumeROI ${FIXED_IMAGE_ROI} --movingVolumeROI ${MOVING_IMAGE_ROI} \
  --numberOfHistogramBins 50 --numberOfMatchPoints 10 --debugNumberOfThreads 4

Note: all parameters are the default settings except numberOfIterations (default 1500), maskProcessingMode (default NOMASK).

FSL FLIRT

flirt -in ${TIME_POINT_2} -ref ${TIME_POINT_1} -omat ${FLIRT_TRANSFORM} -out ${RESAMPLED_IMAGE} -dof 6 -v
  • execution time: ~4 min

Parameter exploration

Validation and accuracy assessment

Results

Conclusions