Hi Beatriz,

I am wondering if I am not receiving all the SPHARM outputs. From the paper: Framework for Statistical Shape Analysis of Brain Structures using SPHARM-PDM, they listed the outputs they get from the pipeline (which includes StatNonParamTestPDM). I see that they had outputs that include covariance results and the text files that store Hotelling T^2 mean difference metric as well as the r^2 stats. However through shapeMANCOVA, I only have the outputs for the distance and vector maps and the p-values. How do I compute for the covariance?

I have a question regarding the results that I computed last week between two different patient's aneurysm cases. Each patient has several aneurysm scans. Aneurysms vary in shapes entirely unlike caudate. It is strange that when I compared scans from the same patient, the distance map shows many areas P < 0.05 while comparing scans from two difference patients, the distance map rarely has any significant spots. However, the vector maps do make sense in terms of length and much more variations in directions for the two diff patients.

Last question regarding the -paraOut option. After the ParaToSPHARMMeshCLP command, I get the a a paraMix, paraPhiHalf, paraPhi, and paraTheta output. I understand I can use the paraPhi and paraTheta for QC purposes. What is the paraMix and paraPhiHalf?

Cheers,
Sylvia