Dear Freesurfer Team,
I am facing a discrepancy in the result when I run a Monte Carlo Z simulation. I have a group with 3 levels(normal,Non-psychotic and psychotic).I tried running an analysis to c the variation in cortical thickness between the same groups in the QDEC GUI,but since iit was impossible to do so and reading a few similar instances on the Freesurfer mailing list,I decided to run the analysis in Command line using mri_glmfit after mris_preproc.The detailed instructions I followed was from the below mentioned page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis However,Published literature with similar cases has ran the simulation using pairing method i.e, lets say in this case between normal-psychotic,normal-non-psychotic and psychotic-non-psychotic. I have done both the methods to compare,However,I have the opposite results and discrepancy in results. (If there was a negative correlation between normal-psychotic in GUI, there was a positive correlation between normal-psychotic in the Command line analysis). Kindly note that the simulation was run for MC-z 1.3(0.05) in both GUI and Command line. Please help me with this issue and which is the TRUE result.