GWPC

This repository contains the code used for the analyses described in our manuscript "Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders" (Preprint: https://doi.org10.1101/750117).

We used this code to analyse the grey-white contrast in Autism Spectrum Disorder using magnetic resonance imaging from ABIDE 1&2 datasets (http://fcon_1000.projects.nitrc.org/indi/abide/).

Dependencies

FreeSurfer, surfstat, RFT_FDR, R, Python and Octave are needed for the whole process. One can create a directory bin/modules and put surfstat and RFT_FDR in.

Octave

• add the modules to ~/.octaverc (you may need to adapt surfstat and RFT_FDR paths to match yours):

echo "addpath('$PWD/bin/modules/surfstat');" >> ~/.octaverc
echo "addpath('$PWD/bin/modules/RFT_FDR');" >> ~/.octaverc
echo "addpath([getenv('FREESURFER_HOME') '/matlab']);" >> ~/.octaverc

• patch the surfstat module to run with octave:

patch -p0 -d bin/modules -i ../../src/freesurfer/surfstat.diff

Preprocessing

Combine and format abide 1&2 tables for GLM analyses:

Rscript src/preprocessing/prepare_phenotypes.R

Run FreeSurfer recon-all pipeline on each subject:

recon-all -subjid $subjid -i $subjanat -autorecon-all

Compute grey/white matter contrast at different levels and cortical thickness for each subject:

bash src/preprocessing/resample.sh $subjdir

Compute BSC (boundary sharpness coefficient) values for each subject:

bash src/preprocessing/bsc.sh $subjdir

Analyses

To run FreeSurfer GLM, adapt src/freesurfer/run_glm_config.sh and run:

bash src/freesurfer/run_glm.sh src/freesurfer/run_glm_config.sh

To get cluster-wise statistically significant clusters with RFT and Monte Carlo simulations, adapt src/freesurfer/correct_glm_config.sh and run:

bash src/freesurfer/correct_glm.sh src/freesurfer/correct_glm_config.sh

To plot the figures of the effect for each contrast, adapt src/freesurfer/plot_figures_config.py and run:

python3 src/freesurfer/plot_figures.py