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 adaptsurfstatandRFT_FDRpaths 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