Quantification 0.0.1 http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWModeling Slicer Andriy Fedorov (SPL/BWH) This work was partially funded by NIH grants R01 CA160902 (PI Maier) and U24 CA180918 (PIs Kikinis/Fedorov). Input Input parameters imageName Input image input Input DWI MRI trace multivolume image 0 modelName model Model Select the mathematical model used to fit the data BiExponential MonoExponential BiExponential Kurtosis Gamma StretchedExponential maskName mask Input mask input Input mask. Optional; if not specified, fitting will be done at all voxels. bValuesToInclude B-values to include bvalInclude List of integers corresponding to the b-values that should be included in fitting data. Note that only one of the two lists (inlusion or exclusion) should be populated, or both can be empty, in which case all b-values will be used. Optional; if not defined, all b-values will be used. bValuesToExclude B-values to exclude bvalExclude List of integers corresponding to the b-values that should be excluded from fitting data. Note that only one of the two lists (inlusion or exclusion) should be populated, or both can be empty, in which case all b-values will be used. Optional; if not defined, all b-values will be used. Output common to all models fittedVolumeFileName fittedVolume Fitted volume Output volume containing the values of the fitted function output rsqrVolumeFileName rsqrVolume R^2 quality of fit volume Output volume containing the R^2 measure of the quality of fit. This measure is calculated only for the b-values used in the fitting process. output ssdFittedVolumeFileName ssdFittedVolume SSD for the fitted b-values Volume with the pixel-wise sum of squared differences (SSD) map that takes into consideration only those b-values that were used in the fitting process output ssdVolumeFileName ssdVolume SSD for all b-values Volume with the pixel-wise sum of squared differences (SSD) map that takes into consideration all b-values. Note that this map will be identical to the previous one if the fitting procedure utilized all b-values output csFittedVolumeFileName csFittedVolume Chi squared for the fitted b-values Volume with the pixel-wise chi squared map that takes into consideration only those b-values that were used in the fitting process output csVolumeFileName csVolume Chi squared for all b-values Volume with the pixel-wise pixel-wise chi squared map that takes into consideration all b-values. Note that this map will be identical to the previous one if the fitting procedure utilized all b-values output MonoExponential model output adcMapFileName adcMonoExpDiff MonoExp diffusion map output Diffusion coefficient map of the mono-exponential model BiExponential model outputs slowDiffMapFileName slowDiff Slow diffusion map output Slow diffusion coefficient map of the bi-exponential model fastDiffMapFileName fastDiff Fast diffusion map output Fast diffusion coefficient map of the bi-exponential model fastDiffFractionMapFileName fastDiffFraction Fast diffusion fraction map output Fast diffusion fraction map of the bi-exponential model Kurtosis model outputs kurtosisDiffMapFileName kurtosisDiff Kurtosis diffusion map output Diffusion coefficient map of the kurtosis model kurtosisMapFileName kurtosis Kurtosis map output Kurtosos map Gamma distribution model outputs See Oshio et al. 2014 thetaMapFileName theta Theta parameter map output Theta parameter of the gamma distribution model kMapFileName k k map output k map of the gamma distribution model modeMapFileName mode Mode map output Mode map of the gamma distribution model ( (k-1)*theta ) Stretched exponential model outputs See Bennett et al. 2003 DDCMapFileName ddc DDC map output Distributed Diffusion Coefficient map alphaMapFileName alpha Stretching parameter map output Stretching parameter (alpha) map Initialization Model-specific initial parameters monoExpInitParameters Mono-exponential model monoExpInitParameters List of initial model parameters in the following format (all numbers are floating point):initialScale,initialADC 0,0.0015 biExpInitParameters Bi-exponential model biExpInitParameters List of initial model parameters in the following format (all numbers are floating point):initialScale,initialFastDiffusionFraction,initialSlowDiffusionCoefficient,initialFastDiffusionCoefficient 0,0.7,0.00025,0.002 kurtosisInitParameters Kurtosis model kurtosisInitParameters List of initial model parameters in the following format (all numbers are floating point):initialScale,initialKurtosis,initialKurtosisDiffusion 0,1,0.0015 stretchedExpInitParameters Stretched exponential model parameters stretchedExpInitParameters List of initial model parameters in the following format (all numbers are floating point):initialScale,initialDDC,initialAlpha 0,0.0017,0.7 gammaInitParameters Gamma distribution model gammaInitParameters List of initial model parameters in the following format (all numbers are floating point):initialScale,initialK,initialTheta 0,1.5,0.002