MeningiomaMRIRegistrationStudy

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.
• images were acquired with the same sequence, but possible on different scanners, all scans are axial
• 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
• minimum tuning of registration parameters (is this possible? to answer this sub-question we compare the results with FLIRT registration using its default parameters)

Methods

Registration

BRAINSFit

• BRAINSFit on NITRC
• Technical details on InsightJournal
• Parameters:

${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).

• execution time: ~12 min

FSL FLIRT

• FSL FLIRT
• Technical details
• parameters:

flirt -in ${TIME_POINT_2} -ref ${TIME_POINT_1} -omat ${FLIRT_TRANSFORM} -out ${RESAMPLED_IMAGE} -dof 6 -v

• execution time: ~4 min

Results

BRAINSFit

• • Case01

• 
• 
• 

• • Case03

• 
• 
• 

• • Case04

• 
• 
• 

• • Case10

• 
• 
• 

FSL FLIRT

• • Case01

• 
• 
• 

• • Case03

• 
• 
• 

• • Case04

• 
• 
• 

• • Case10

• 
• 
•