Codes related to the study "Boosting rTMS-induced cortical plasticity with high-gamma theta-burst stimulation"

Readme MEP analysis EMG_SCRIPT.m – First plot all MEPs overlayed per session to find the latency of the MEP -> identify the time window that captures the MEP without noise. P2P_processing_SCRIPT.m – Input the individual time window identified from the first script individually for each session and run this script to extract all MEP amplitudes per subject per session. All MEP amplitudes were extracted and combined into a single excel file, removing outliers (+-3SD) was performed manually followed by averaging and normalizing MEP amplitudes. fMRI processing fMRI_Preprocessing_Prisma_DCM2NII.m – Run SPM12’s standard preprocessing pipeline on raw .nii files (script converts dcm to nii if not already performed) https://miplab.epfl.ch/software/icaps-toolbox - Run the total activation pipeline from the iCAPs toolbox. [Following steps were performed manually with command-line arguments] - Run fslsplit on preprocessed, unsmoothed .nii file [Total activation needs each volume as a separate file] - Edit the Inputs_TA_DATA_OpenfMRI.m script with paths - Run main_TA.m -> outputs Activity_inducing.nii file - Due to reduced brain coverage from the two dedicated MR coils, cropping needs to be applied to the outputs to conserve covered regions: fslroi mask_brain.nii crop_mask3.nii 0 -1 0 -1 43 91 - Apply 5x5x5 smoothing with nilearn’s smooth function: smoothed_img = image.smooth_img(func_img, fwhm=5) fMRI analysis Nilearn was used to run the first and second level analyses. 1stLevel.ipynb – Performs the first level analysis on all subjects / sessions Second level analyses were then performed on each stimulation group individually (100Hz iTBS, 50Hz iTBS, or sham) with the respective scripts: 2ndLevel_100Hz.ipynb, 2ndLevel_50Hz.ipynb, 2ndLevel_sham.ipynb.