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If you have any questions, please refer to the University's data classification guide or contact ict.askcyber@sydney.edu.au
Analysis
- Chengtao Liang (Unlicensed)
Cortical & subcortical ROI analysis
FreeSurfer automatically segments and parcellates the whole brain into ROIs according to the Desikan/Killiany atlas. Volumes and thickness of these ROIs can be obtained by using the anatomical ROI analysis.
You can also analyse the ROI data using a different program by exporting the cortical thickness of cortical ROIs and volumetric data of subcortical ROIs.
Hippocampal subfields and nuclei of amygdala analysis (cross-sectional and longitudinal)
FreeSurfer v6.0 and above automatically segments the hippocampus and amygdala to smaller subregions. A guide on how to process and analyse these regions are outlined here.
QDEC
QDEC is a GUI-based application within FreeSurfer that can perform cortical surface and volume analysis between subjects and groups using GLM.
GLM analysis using command line
This analysis is similar to QDEC, however, using the command line provides more flexibility on the contrasts that you can perform. Click here for the official FreeSurfer guide on group analysis.
Longitudinal data - Two stage model (two timepoints)
Longitudinal two stage model is ideal for modelling longitudinal data with 2 time points (baseline and follow-up). This analysis requires longitudinal pre-processing to be completed.
Longitudinal data - Linear mixed effects
Linear mixed effects modelling is very powerful for analysing longitudinal data with variable time points. Click here for the official guide on longitudinal linear mixed effects modelling in FreeSurfer. This analysis requires longitudinal pre-processing to be completed, and uses both Matlab and FreeSurfer to generate results.
Visualisation using freeview
Freeview is the primary program used within FreeSurfer for visualisation. It can be used to visualise raw data, edit data during pre-processing and visualise results of volumes and cortical thickness.
Visualisation using tksurfer
tksurfer is a useful tool for visualisation of cortical surface data. This tool is ideal for creating/editing ROIs and creating images for final results.