DBS fMRI Reproducibility Repository

This repository contains de-identified example data and resources for assessing the reproducibility of resting-state fMRI (rs-fMRI) scans in Parkinson's patients who are receiving deep brain stimulation (DBS) therapy. It includes code and patient-derived, de-identified data for analysis and processing. The repository is part of ongoing research in the Radiology-Morrison-lab-UCSF.

Contents

• testretest_ICC.m:

  • Code to calculate intraclass correlation coefficient (ICC) values between test and retest resting-state fMRI scans using functional connectivity and brain variability data, as well as corresponding statistical analyses in the lab's paper, This script works in conjunction with the ICC function (Salarian 2024): https://www.mathworks.com/matlabcentral/fileexchange/22099-intraclass-correlation-coefficient-icc .

• testretest_ICC_affectofmetalartifact.m:

  • Code to create a map of DBS electrode spatial trajectories and identify intersecting brain regions using T1-weighted MRI scans and rs-fMRI scans. Once intersecting regions are identified, the code calculates ICC values between test and retest resting-state fMRI scans of two subsets of brain regions: those affected by the electrode and those unaffected. Finally, the code conducts corresponding analyses in the lab's paper, "Test-retest reliability of resting-state functional magnetic resonance imaging during deep brain stimulation for Parkinson’s disease".

• testretest_ICC_betweensessions.m:

  • Code to calculate ICC values between longitudinal test and retest resting-state fMRI scans, as well as conduct corresponding analyses from the lab's paper, "Test-retest reliability of resting-state functional magnetic resonance imaging during deep brain stimulation for Parkinson’s disease".

• testretest_makeconnectomes.m:

  • Code to calculate functional connectivity AND brain variability values, as well as conduct corresponding analyses from the lab's paper, "Test-retest reliability of resting-state functional magnetic resonance imaging during deep brain stimulation for Parkinson’s disease".

• AdvMRIforDBS_InternalProtocol--2025.pdf:

  • Advanced MRI for DBS: Internal UCSF Protocol for 3T Brain MRI with DBS implant.

• MDS-UPDRS_Scores_Template.xlsx:

  • ​An Excel template demonstrating MDS-UPDRS score calculations with dummy data. ​

• testretest_ROIs.xlsx:

  • A list of ROIs used for the whole brain, motor, limbic, and associative networks.

• testretest_demographics.xlsx:

  • An Excel sheet containing cross-sectional patient data, including demographics, DBS specifications, Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) sub-scores, and Levodopa Equivalent Daily Dose (LEDD) scores.-

• FC_BV_Data:

  • A folder containing all of our functional connectivity (FC) and brain variability (BV) data as .mat files.

• atlases:

  • A folder containing atlas files and their adjoining ROI text files for region identification.

• otsu-segmentation:

  • A folder containing code to run Otsu's method for image thresholding.

• Data:

  • All de-identified MRI scans and associated metadata will be made publicly available through OpenNeuro upon completion of ongoing analyses.

License

• Copyright 2025 UCSF
• Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
• FC_BV_Data and testretest_demographics.xlsx were acquired at the University of California San Francisco and are licensed under the CC BY-NC 4.0 license

Acknowledgments

This project is part of ongoing research in the Radiology-Morrison-lab-UCSF. Special thanks to all contributors and collaborators involved in this work.