Hi Dear Beatriz,
 
Thanks a lot for getting back to me, your comprehensive reply and valuable tips and also very grateful for your explanation about registration.
 
At this point, I want to have a quick and integrated overview of the steps in the shape analysis with SPHARM.
As you mentioned in the last answer, I am doing the following steps in two ways.
First way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select groups".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select groups".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is appeared.
4- I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- A window is opened that contains a message: "Do you want to open Slicer with the Mrml scene already loaded?" I click on Yes button. I must mention that I installed Slicer3 (Slicer3-3.6.3-2011-03-04-linux-x86_64) in addition to the Slicer4 (Slicer-4.5.0.1-linux-amd64) in my computer.  At this time, Slicer3 is opened and I get the message of "Slicer had trouble loading the scene file. Scene may contain empty datasets." and nothing happened?! How can I create Mrml scene? In other words, what outputs (for example *_pp_para.vtk, *_pp_surfSPHARM.vtk, *_pp_surfSPHARM.coef, *_pp_surfSPHARM_ellalign.vtk, *_pp_surfSPHARM_ellalign.coef and   *_pp_surfSPHARM_procalign.vtk) should I use to create Mrml scene? and how?
 
Second way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select input file column".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select input file column".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is NOT appeared!!
4- Anyway, I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- After a few moments, the following files and folder are created in the folder that contains csv file (ShapeAnalysisModule_OutputFile.csv file):
ShapeAnalysisModule_OutputFile.csv
ShapeAnalysisModule_OutputFile.csv_commandline.txt
ShapeAnalysisModule_OutputFile.csv_DiffMagnitude.txt
ShapeAnalysisModule_OutputFile.csv_diffMesh.txt
ShapeAnalysisModule_OutputFile.csv_GLM_correctedMean.meta
ShapeAnalysisModule_OutputFile.csv_mancovaBonferroniP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaFDRP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaRawP.txt
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.meta
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.vtk
ShapeAnalysisModule_OutputFile.csv_meanA.meta
ShapeAnalysisModule_OutputFile.csv_meanB.meta
ShapeAnalysisModule_OutputFile.csv_normProjections.txt
transformFiles (empty folder)
 
7- At this time, Slicer3 is opened and nothing happened!! Why? What is the application of the outputs mentioned above?
 
Please guide me.
Best regards,
Shahrokh