This repository provides the analysis pipeline and documentation for our study:
“Multimodal Characterisation of Subcortical Networks in Tinnitus”
The project investigates structural and functional connectivity in tinnitus by comparing the cortical and subcortical organization of tinnitus patients and healthy controls.
We combine structural MRI (sMRI), diffusion MRI (dMRI), and resting-state fMRI to characterise both the brain’s structural wiring and functional networks.
The pipeline supports preprocessing of structural, functional, and diffusion MRI data by integrating established tools such as FreeSurfer, FSL, ANTs, and MRtrix. It also facilitates atlas handling—projecting atlases like Schaefer, Glasser, and Tian subcortical atlases into each subject’s native space—and provides a complete workflow for cortical and subcortical tractography, enabling the construction of structural connectomes across both cortical and subcortical regions.
The processing scripts are numbered to indicate their execution order. Each script name follows the pattern ant_{i}_*, where {i} is the step number.
| Step | Script | Description |
|---|---|---|
| 0 | ant_00_* |
Creates the project directory structure and organizes raw sMRI, fMRI, and dMRI data acquired on the Philips MRI scanner at University Hospital Zurich. |
| 1 | ant_01_* |
Runs FreeSurfer recon-all in parallel on the structural MRI data to produce the SUBJECTS_DIR for FreeSurfer. |
| 2 | ant_02_* |
Uses FreeSurfer Bayesian segmentation tools to subsegment the hippocampus, amygdala, thalamic nuclei ascending arousal network (AAN), and register the Schaefer and Glasser atlas. to both surface and volume. |
| 3 | ant_03_* |
Performs tractography at both population and individual levels to generate global and subcortical structural connectivity (SC) matrices. |
| 4 | ant_04_* |
Jointly segments thalamic nuclei using combined T1 and dMRI data. |
| 5 | ant_05_* |
Applies Pierrick Coupé’s non-local means algorithm to denoise structural MRI data prior to downstream fMRI analysis. |
| 6 | ant_06_* |
Handles fMRI preprocessing and denoising for both sessions. |
For questions or collaboration inquiries, please contact payam.