NIH Blueprint: The Human Connectome Project

Exploring the Human Connectome

HCP Course Practical Data and Software

Unfortunately, due to University-wide network changes, the 2016 HCP Course Practical Data and Software is no longer available as a downloadable Virtual Machine (VM). We expect to be able to remedy this situation for distribution of the 2019 course VM.

Course Schedule

Day 1: Sunday, Aug 28

TypeCourse (Presenter)Resources
WelcomeIntro and Overview (David Van Essen)PDF:
LectureHCP Data Acquisition (Michael Harms)PDF:
PracticalIntroduction to wb_view (Jenn Elam)PDF:
LectureStructural MRI: Precise Neuroanatomical Localization (Matt Glasser)PDF:
LectureData Quality (Michael Harms)PDF:
PracticalData Quality (Michael Harms)PDF:
LectureGroup Brain Parcellation (Matt Glasser)PDF:
PracticalIntroduction to wb_command and Group Parcellation (Tim Coalson, Jenn Elam)PDF:

Day 2: Monday, Aug 29

TypeCourse (Presenter)Resources
LectureMultimodal Classification of Areas in Individuals and Parcellation Validation (Matt Glasser)PDF:
PracticalIndividual Brain Parcellation (Matt Glasser)PDF:
LecturerfMRI background, Preprocessing, Denoising (Steve Smith)PDF:
LecturerfMRI Temporal Noise (Steve Smith, Matt Glasser)PDF:
PracticalrfMRI Preprocessing, Denoising; ICA-based Parcellations (Steve Smith)PDF:
LecturerfMRI Network Analysis Strategies (Steve Smith)PDF:
PracticalrfMRI Netmats and Dual Regression (Steve Smith)PDF:

Day 3: Tuesday, Aug 30

TypeCourse (Presenter)Resources
LectureHCP Pipelines (Tim Brown)PDF:
PracticalHCP Pipelines Practical (Tim Brown)PDF:
LectureRegression, Prediction, and Permutation Analyses (Thomas Nichols, Anderson Winkler)PDF:
LectureFamily Structure and Heritability (Thomas Nichols)PDF:
LectureTask fMRI and Behavioral Measure Analyses (Greg Burgess)PDF:
PracticaltfMRI and PALM (Greg Burgess, Anderson Winkler)PDF:
LectureHCP Informatics (Daniel Marcus)PDF:
LectureUnderstanding the Clinical Connectome: Application of HCP Methods to Neuropsychiatric Illness (Alan Anticevic)PDF:

Day 4: Wednesday, Aug 31

TypeCourse (Presenter)Resources
LectureDiffusion MRI, Distortion Correction and DTI (Jesper Andersson)PDF:
PracticalDiffusion MRI, Distortion Correction and DTI Practical (Jesper Andersson)PDF:
LectureFibre Orientation Models and Tractoghraphy Analysis (Michiel Cottar)PDF:
PracticalFibre Orientation Models and Tractography Analysis Practical (Michiel Cottar)PDF:
PracticalTractography and Tracer (Chad Donahue)PDF:
LectureCloud-based Processing (Daniel Marcus)PDF:
PracticalCloud-based Processing Using HCP Pipelines and Amazon Web Services (Tim Brown)PDF:

Day 5: Thursday, Sep 1

TypeCourse (Presenter)Resources
LectureIntroduction to HCP-MEG Connectome (Linda Larson-Prior)PDF:
PracticalMEG Preprocessing, Channel and Source Analysis of tMEG and rMEG (Giorgios Michalareas, Franceso di Pompeo)PDF:
LectureMEG Connectivity and Follow-up Analyses for HCP MEG Data and Other Software Tools (Robert Oostenveld)PDF:
PracticalrMEG and tMEG Source-level Connectivity; Multimodal Integration (Giorgios Michalareas, Franceso di Pompeo)PDF:
PracticalBuilding wb_view scenes and sharing on BALSA (Jenn Elam)PDF:
LectureHCP and Beyond: Looking Back and Forward (David Van Essen)PDF:

Course Description

On This Page:

Learn about multi-modal neuroimaging data, analysis, and visualization tools of the Human Connectome Project

We are pleased to announce the 2016 HCP Course: "Exploring the Human Connectome", to be held Aug 28 – Sep 1 at the Joseph S Martin Conference Center at Harvard Medical Center, in Boston, Massachusets, USA.

This course is designed for investigators who are interested in:

  • using data being collected and distributed by HCP
  • acquiring and analyzing HCP-style imaging and behavioral data at your own institution
  • processing your own non-HCP data using HCP pipelines and methods
  • learning to use Connectome Workbench tools and the CIFTI connectivity data format
  • learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data
  • positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease)

This 5-day intensive course will provide training in the acquisition, analysis and visualization of freely-available data from the Human Connectome Project using methods and informatics tools developed by the WU-Minn HCP consortium. Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data.  Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. 

The course is open to graduate students, postdocs, faculty, and industry participants.  The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including familiarity with FSL and Freesurfer software.  

All lectures and printed material will be in English.


Speakers: David Van Essen, Matt Glasser, Michael Harms, Steve Smith, Tom Nichols, Anderson Winkler, Greg Burgess, Dan Marcus, Alan Anticevic, Jesper Andersson, Michiel Cottaar, Chad Donahue, Robert Oostenveld, Linda Larson-Prior

Practical Tutors: (in addition to speakers): Jenn Elam, Gordon Xu, Tim Brown, Tim Coalson, Giorgos Michalareas, Francesco Di Pompeo

Contact Information

If you have any questions, please contact us at:

We look forward to seeing you in Bah-ston!