[Freesurfer] Harmonization (Site/Scanner) for FreeSurfer Area Data

External Email - Use Caution Hi FreeSurfer experts, I have harmonized across site and scanners on both thickness and area for a large cohort (500+ subjects). We are seeing high covariance values when comparing the harmonized and non-harmonized area datasets and trying to

[Freesurfer] GLM Using 2 Surfaces - Thickness and Area

External Email - Use Caution Hello Freesurfer team, I am interested in doing one glm analysis using both the thickness and cortical surface area. My question is two-fold: First, is it possible to provide both the thickness and area files to mris_preproc and mri_surf2surf

[Freesurfer] Correlation Line Plot for FS Group Analysis

External Email - Use Caution Hello, I am to generate a plot to visualize the slopes between classes for group analysis. I would like to generate something similar to this freesurfer post:

[Freesurfer] Group Analysis - 4 groups 3 covariates

External Email - Use Caution Hi, I would like to run a group analysis on 4 groups (patientM, patientF, controlM, controlF) with 3 covariates (age, cogscore1, cogscore2). I am running with dods - so I would have 16 total regressors. How would I create contrast matrices for