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Minicourse EDDA-ES08

Diffuse Optical Mapping of Human Brain Function using NIRFAST and NeuroDOT: A Hands-on course

Emma Speh

with Adam Eggebrecht, Hamid Dehghani, Ari Segel

About this course

This course will provide practical knowledge for understanding the physics behind diffuse optical human brain mapping along with hands-on experience with powerful tools for data analyses. The course will be composed of three lectures along with two in-depth hands-on sections to provide both background and experience the attendee can take with them to use on their own data. This includes how near-infrared light propagates in tissue and how to model it using the freely distributed NIRFASTer software package, a widely-used, user-friendly package for modeling NIR light propagation in tissue and recovering images of optical parameters in arbitrarily-shaped tissue volumes. Additionally, lectures and hands-on exercises will focus on temporal data processing and image reconstruction using both the workstation- and cloud-based versions of the NeuroDOT software package. Attendees will run and visualize light propagation models of the human head and will also learn and develop skills using image reconstruction algorithms. All the training will be centered upon providing skilled knowledge, training, and practical tools for volumetric imaging of functional brain activations based on contrasts of hemoglobin concentration as measured using Diffuse Optical data. The class will review the basic physics and biology of the approach, step through how the software works, and train attendees to use the software through exercises. More information about NIRFASTer can be found at, and more information about NeuroDOT is available at

Learning Outcomes

  • Explain and model photon propagation in turbid tissue.
  • Set up pipelines for data analyses for system modeling, temporal data processing, and image reconstruction.
  • Perform a range of analyses, locally on a workstation and/or using cloud-based resources on OXI, to assess data quality, brain responses to tasks, and functional connectivity.  

Course Plan

Level: Introductory

Pre-Requisites: Download and install NeuroDOT (follow instructions presented here)
Course Duration: 3 hours

Delivery Plan

20 min: Presentation 1 (Intro to tissue optics and NIRFASTer, presented by Hamid Dehghani).
20 min: Presentation 2 (Preprocessing, Image Reconstruction, and Data Visualization with NeuroDOT, presented by Emma Speh).
45 min: Hands-on 1 (Local data processing with NeuroDOT, led by Ari Segel).
20 min: Presentation 3 (Data processing in the cloud with OXI and NeuroDOT_py, presented by Adam Eggebrecht).
45 min: Hands-on 2 (Cloud-based data processing with OXI & NeuroDOT_py, led by Adam Eggebrecht).
20 min: Q&A with all presenters.

Why enrol on this course?

By enrolling in this course, participants will understand fNIRS and HD-DOT methods, limitations, and interpretation. In addition, they will be able to quantitatively assess and track data quality and sources of spurious variance and perform optical neuroimaging analyses in a reproducible manner.