Welcome to the wiki of my lab! Here are lots of scripts for magnetic resonance imaging (MRI), magnetoencephalography (MEG), and electroencephalography (EEG) research.

Goto the wiki page for further details.

The web sites of our lab are here and here at Sunnybrook.

Contact me if there is any question/error.

Structural MRI

• FreeSurfer reconstruction for brain 3D models and anatomical segementation, labels, parameters .

• FreeSurfer quick sheet

• Diffusion tensor imaging (DTI) analysis

functional MRI (fMRI)

• Stimuli presentation using Psychtoolbox

• Unpack dicom files for analysis.

• fMRI preprocessing includes motion correction, slice timing correction, and spatial smoothing.

• Tasked fMRI analysis uses General Linear Modeling to identify brain regions correlated with a model of stimulatin, task performance, or other explicit (time-domain) models.

• Resting-state fMRI analysis using 'seed-based' correlation to identify a network with correlated fMRI signal dynamics with a chosen brain location.

• Inter-subject correlation analysis of fMRI using complex naturalistic stimuli.

• SMS-InI analysis

• Co-register between SMS-InI reconstructions and anatomical MRI

• Cortical-depth dependent fMRI analysis

EEG-MRI

• Measurement setup

• Data collection cheat sheet

• EEG artifact suppression

• Processing of sample data of steady-state visual evoked potentials

• EEG evoked potentials and source analysis

MEG

• MEG analysis for the data collected at Academia Sinica

Stereotatic EEG (SEEG)

Some pages are from fhlin_toolbox repo.

• Register the location of SEEG electrodes using post-implantation MRI; Step I

• Register the location of SEEG electrodes using post-implantation MRI; Step II

• Register the location of SEEG electrodes using post-implantation CT

• Visualize the registered electrodes I

• Visualize the registered electrodes II

• Data analysis over electrodes

• SEEG source analysis: individual

• SEEG source analysis: group

Transcranial magnetic stimulation

• Image preparation for BrainSight

• Electric field modeling

• Electric field modeling with interactive TMS coil placement

Bruker 7T animal MRI

• Data collection

Visualization

These are pages from fhlin_toolbox repo.

• Show 3D brain model for an individual

• Show 3D brain model and orthogonal slicse for an indvidual. This includes showing cortical labels created automatically by FreeSurfer (.annot file).

• Show and create a region-of-interest on a 3D brain model.

• Show 3D brain model with cortical labels. These labels are either from individual label files (*.label) or a collection of labels in an annotation file (.annot).

• Show 3D brain model with overlay. The overlay is typically fMRI results, which is a static image here.

• Show 3D brain model with dynamic overlay. The overlay is typically fMRI results, which can be a static image or a collection of images over time.

• Show or examine the spatial co-registration between structural MRI and fMRI

Sample data

• EEG-MRI: steady-state visual evoked potentials

• fMRI: Physiological noise in healthy elderly and Alzheimer's disease patients

• fMRI: perspective-taking effects probed by movies

• EEG: Social perception in young adults and ADHD patients probed by movies

• SEEG: music listening

• EEG-MRI: music listening

• MRI: Human Connectome Project young adults

MRI coils

• Coil housing printing

• Coil test rig for selective detuning

• 3T receiver coil circuits

• Impedance matching circuits for 3T and 7T

• Siemens Tim 4G coil files

• 3T receiver coil bench testing