Interesting questions form Panos about group analysis with SPHARM-PDM tool:
I am trying to compare regional differences in hippocampal structure between three groups (2 diseased groups, and one healthy control group), and I’m having some trouble with the pipeline.
I have volumetric binary files of the hippocampus for each subject (within each group). I used the Shape Analysis Module in SlicerSALT to process each one of those files, and the result was three subdirectories: Step1_SegPostProcess, Step2_GenParaMesh, and Step3_ParaToSPHARMMesh in my subject directory.
What would be the next step in order to statistically compare the regional differences between the three groups? Does SPHARM-PDM do the statistical analysis, or is there another software I should download? Also, do I need to create average volumes before I do any sort of statistical analysis or is the software itself going to take care of that?
For now, in order to statistically compare the regional differences between two models, you can apply the module ModelToModelDistance (available as a module of 3DSilcer): it will compute a distance map between two models with the option corresponding_point_to_point (which will compute the distance euclidean for each corresponding point of your two models). You can then visualize the distance map in ShapePopulationViewer (available in SlicerSALT and 3DSlicer) by displaying the attribute PointToPointVector.
If you want to compare the average group models to each other, you should create an average model of each of your group by using ShapeVariationAnalyzer (available as a module in 3DSlicer) before to apply ModelToModelDistance. The real purpose of this module is not really to compute mean of a population of models but it contains this option. First step is to create a CSV file by using the first tab of the module “Creation of CSV file” and then create your average models by using the tab “Compute of mean group”.