ADC map registration

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ADC map registration

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Dear Slicer users,

I'm using Brainsfit to register ADC maps. I scanned 5 times to the same volunteer in order to obtain the repatability of these maps.

Even using immobilizer small movements and rotations appear so I need to register all the images. Since the slice thickness is 5 mm for those ADC maps I suppose that I cannot expect very good results from the registering process.

A T1 weighted image with 1 mm3  per voxel was scanned in the same session (to be used for freesurfer) so I tried to use it as fixed image in my second attempt instead of the first ADC map.

I used rigid rotations but the results that I obtained seemed like needing an additional BSpline non rigid registration. I used MSE for the first attemp and MMI for the second one with the structural image as fixed one.

Since the results do no seem to be as good as I expected, do any of you have experience enough to tell me if these parameters are correct?

                 '--maskProcessingMode ROI',
                 '--fixedBinaryVolume mask.nii.gz --movingBinaryVolume mask.nii.gz',
                 '--useRigid --use BSpline',              
                 '--samplingPercentage 0.05 --initializeTransformMode Off',
                 '--splineGridSize 4,4,4 --maxBSplineDisplacement 10',
                 '--medianFilterSize 0,0,0 --removeIntensityOutliers 0 --outputVolumePixelType int',
                 '--backgroundFillValue 0 --interpolationMode WindowedSinc',
                 '--numberOfIterations 1500 --maximumStepLength 0.5 --minimumStepLength 0.001',
                 '--relaxationFactor 0.5 --translationScale 1000',
                 ' --reproportionScale 1 --skewScale 1',
                 '--numberOfHistogramBins 50 --numberOfMatchPoints 10',
                 '--costMetric MMI',  #MSE for ADC/ADC
                 '--ROIAutoDilateSize 0 --ROIAutoClosingSize 9',
                 '--costFunctionConvergenceFactor 1000 --projectedGradientTolerance 0.0001',
                 '--maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25',
                 '--metricSamplingStrategy Random',
                 '--fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0',
                 '--maskInferiorCutOffFromCenter 1000  --numberOfSamples 0 --failureExitCode -1 --numberOfThreads -1',
                 '--debugLevel 0 --echo'

Rigid registration finished after 35-40 iterations and non-rigid registration used around 25 iterations.

Do any of you have any suggestion about these parameters?

Thank you in advance.