July 8, 2020
Written by Chi-Hua Chen and Donald Hagler
Adapted by Michael Lombardo
Use this protocol for the analysis of mean cortical thickness and surface area data within fuzzy cluster ROIs defined based on genetic correlations for the UK Biobank.
First get the GitHub repo.
cd ~/code
git clone https://github.com/mvlombardo/GCLUST.git
The _run_gclust_parcellation.sh script should be the main one you should use.
You might need to change paths to where your data is located though...
At the end of this script is the call to sbatch to run it in parallel.
The script it calls that does the main bulk is called gclust_sub.sh. This
script runs some steps in Freesurfer first, and then goes into MATLAB to run
gclust_sub.m for the actual extraction of values for each parcel.
The script intends to run the extraction of GCLUST surface area and thickness
for each individual subject. The end result should be a gclust_area*.csv or
gclust_thickness*.csv file in the surface_area and cortical thickness
directories.
In each of the two files called gclust_thickness.csv and gclust_area.csv there should be 25 columns in each file (the first column is Subject ID, then 12 ROIs for the left hemisphere and 12 ROIs for the right hemisphere). The values in the csv files are already adjusted for global effects.
If these genetically based parcellations for surface area and cortical thickness were used, please cite the following papers.
- Hierarchical genetic organization of human cortical surface area. Chen CH, Gutierrez ED, Thompson W, Panizzon MS, Jernigan TL, Eyler LT, Fennema-Notestine C, Jak AJ, Neale MC, Franz CE, Lyons MJ, Grant MD, Fischl B, Seidman LJ, Tsuang MT, Kremen WS, Dale AM. Science. 2012
- Genetic topography of brain morphology. Chen CH, Fiecas M, Gutierrez ED, Panizzon MS, Eyler LT, Vuoksimaa E, Thompson WK, Fennema-Notestine C, Hagler DJ Jr, Jernigan TL, Neale MC, Franz CE, Lyons MJ, Fischl B, Tsuang MT, Dale AM, Kremen WS. PNAS. 2013