# README This data repository contains the raw and analysed data supporting the findings in "Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans", Yaakub et al., 2023. bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2023.01.20.524869v1 ## Overview The study investigated transcranial ultrasound stimulation (TUS)-mediated changes in brain functional connectivity and neurochemistry using magnetic resonance imaging (MRI). Data were collected at the Brain Research & Imaging Centre in Plymouth, UK, between January and May 2022. For more information, please see paper (https://www.biorxiv.org/content/10.1101/2023.01.20.524869v1) and OSF pre-registration: https://osf.io/bcf4v ## Contact persons If you require more information about the dataset or additional data not available here, please contact: - Dr Elsa Fouragnan (email: elsa.fouragnan@plymouth.ac.uk) - Dr Siti N. Yaakub (email: siti.yaakub@plymouth.ac.uk) ### Dataset summary - Number of participants: 24 healthy control adults - Number of sessions: 4 sessions per participant - Datasets: Magnetic resonance imaging (MRI) data including T1-weighted anatomical, BOLD resting-state functional, MEGA-PRESS spectroscopy ## Raw data - Each subject has 4 sessions, labelled ses-0, ses-1, ses-2 and ses-3 - Sessions 1-3 contain raw anatomical (anat), functional (func) and spectroscopy (mrs) data - Session 0 contains only anatomical data (anat) - participants.tsv and participants.json contains the list of participant IDs, age, sex and TUS randomisation order ## Processed & analysed data: ### acoustic_simulations - The code to run our transducer- & site-specific k-Wave simulations are available at https://github.com/sitiny/BRIC_TUS_Simulation_Tools - Free-field acoustic simulations were run using tussim_water_3D.m (phase of each element obtained from the NeuroFUS TPO based on focal depth) to obtain source magnitude required for each focal depth - T1-weighted MR used in the simulations are from raw data ses-0/anat - acoustic_sims.xlsx: contains the parameters to run the simulations (Neuronavigation parameters) and the output of the simulations (Simulated output) - pseudo-CT: pseudo-CT images used in the simulations - produced using the mr-to-pct toolbox: https://github.com/sitiny/mr-to-pct - focal_volumes: the output binary focal volume from simulations ### mrs_analysis - TWIX_SpecReg_QC_clean.xlsx: output of processed MRS data (after QC). - voxel_mask: contains the location of dACC and PCC voxels placed in each subject during each session. - GLM_dACC.pdf: results of the ANCOVA on dACC GABA+/Water values - GLM_PCC.pdf: results of the ANCOVA on PCC GABA+/Water values - matlab_plot: values and code snippet to plot Figure 4 in the paper ### fmri_analysis - The preprocessed functional data, subject-specific TUS-based seed ROIs and registration transforms are given for each subject and session - group-level/bg_image_meansubs.nii.gz: the mean of T1w MRIs for all subjects - group-level/group_seedbased-dACC: seed-based analyses for the dACC seed - group-level/group_seedbased-PCC: seed-based analyses for the PCC seed - group-level/melodic_dualreg: group ICA + dual regression analysis - group-level/matlab_cluster_plot: values and code snippet to produce spider plots in Figure 5 of the paper ## Notes T1-weighted MR and pseudo-CT images have been de-faced using pydeface (https://github.com/poldracklab/pydeface)