Dear Freesurfer team, 

My colleagues and I performed a general linear model with FreeSurfer mri_glmfit for whole brain analysis in intergroup comparison (g2v1) with a Monte-Carlo correction. 

I'd like to get the effect size of the analysis and I was wondering how could I get the eta squared or R²? I

I also saw that the gamma.mgh file was the contrast effect size. Could this be used as an effect size for this type of analysis? 

I was also wondering if it was possible to plot the results from the GLM and getting a linear regression with the ROI as the y axis and neuropsychiatric symptom severity on the x axis and displaying both groups (Alzheimer vs Mild cognitive impairment) in one plot? If it is possible, how can I do this? I found a plotting script (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization), but it was for FDR corrected, not Monte-Carlo. 

Finally, I was also wondering how could I display a heat map or gradient shading based on neuropsychiatric symptoms severity on the image from the significant regions I got from the GLM with freeview? 

Thank you in advance!
Lyna El Haffaf

Graduate student in neuropsychology 

University of Montreal