GCLUST Phenotype Extraction Protocol

December 3, 2014

Written by Chi-Hua Chen and Donald Hagler

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 Cortical GWAS Meta-Analysis – ENIGMA3.

If you have any questions or run into problems, please feel free to contact us: (chc101@ucsd.edu) and (dhagler@ucsd.edu)

These protocols are offered with an unlimited license and without warranty.
However, if you find these protocols useful in your research, please provide a link to the ENIGMA website in your work: www.enigma.ini.usc.edu

---

Extract FreeSurfer measures with cortical surface genetic clusters

Italicized portions of the instructions may require you to make changes so that the commands work on your system and data.

This section assumes that you have already run the Image Processing Protocols Step 1-3 of ENIGMA3 (http://enigma.ini.usc.edu/ongoing/gwasma-of-cortical-measures/).

NOTE: It is recommended that these analyses be performed on data that have been processed with FreeSurfer v5.3. If your data have not been processed with this version, please consider re-running –autorecon3 with the v5.3 binaries and using those cortical segmentations for this protocol (additional QC should not be required). If for some reason re-analyzing your data is not feasible note that v5.2 and versions prior to v5.0 ARE NOT COMPATIBLE with this protocol. If you have any questions please contact Don (dhagler@ucsd.edu) and Chi-Hua (chc101@ucsd.edu).

---

• Download the all the files in the GCLUST directory:

svn checkout https://github.com/ENIGMA-git/GCLUST/trunk/GCLUST

• Move the directory GCLUST to the parent folder of your FreeSurfer output. For example:

Subject1/	Subject2/	Subject3/	Subject4/	GCLUST

• Within this parent directory, make sure that the fsaverage is available. In the tcsh shell:

setenv FREESURFER_HOME /usr/local/freesurfer-5.3.0_64bit
ln -s ${FREESURFER_HOME}/subjects/fsaverage .

• Change directories (cd) into the GCLUST directory.

---

Create a list of FreeSurfer subject directories to be included in the result spreadsheets using the set_subjlist.csh script.

• Open the set_subjlist.csh script in any text editor and edit the environment variable:

setenv SUBJECTS_DIR /usr/enigma/FSoutput

note: this is where you find the reconstructed freesurfer data for all subjects

• Save changes
• Run the script:

./set_subjlist.csh

Important: This will create a subdirectory called surfdata containing a file called subjlist.txt. Verify that the entries included in this file are correct. Quality Checking: Remove all rows in the resultant subjlist.txt file for subjects that were marked as poorly segmented for the whole subject in Step 2 for Quality Checking of Outputs. Make sure to save the subjlist.txt file.

---

Resample FreeSurfer surface measures to the atlas and extract weighted averages using fuzzy cluster ROIs based on genetic correlations using the gclust.csh script.

• Open the gclust.csh script in any text editor and edit environment variables:

setenv FREESURFER_HOME /usr/local/freesurfer-5.3.0_64bit

setenv SUBJECTS_DIR /usr/enigma/FSoutput

note: this is where you find the reconstructed freesurfer data for all subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh

note: in a typical FreeSurfer setup, you must edit this SetUpFreeSurfer.sh file

• Save changes
• Run the script:

gclust.csh

---

After extracting FreeSurfer measures with cortical surface genetic clusters, you should have 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). All the subjects marked as poorly segmented in the QC Steps were removed. 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, Gutiérrez 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

Feel free to send questions to Don (dhagler@ucsd.edu) and Chi-Hua (chc101@ucsd.edu).