NIH Blueprint: The Human Connectome Project

Exploring the Human Connectome (2015)

HCP Course Practical Data and Software

Unfortunately, due to University-wide network changes, the 2015 HCP Course Practical 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 and Resources

Note: You can download all HCP Course materials en masse from

Day 1 (Monday, 8 June): Structural imaging; preprocessing; intersubject registration; parcellation

Type (Time)CourseResources
Lecture 1 (8:00 - 9:30)Intro & overview (Van Essen) PDF: Day1_Lecture1a_HCP_Course_Intro_VanEssen.pdf
HCP Acquisition Basics (Harms/Xu) PDF: Day1_Lecture1b_HCP_Acquisition_Basics_Harms.pdf
Practical 1 (9:30 - 10:30)Intro to wb_view & Imaging File Types PDF: Day1_Practical1_wb_view&FileTypes.pdf
Lecture 2 (11:00 - 12:00)Structural MRI: Precise Neuroanatomical Localization through Careful Processing (Glasser) PDF: Day1_Lecture2_Structural_MRI_Glasser.pdf
PPT: Day1_Lecture2_Structural_MRI_Glasser.pptx
Practical 2 (1:30 - 3:30)wb_command & HCP pipelines I PDF: Day1_Practical2_wb_command&PipelinesI.pdf
Lecture 3 (3:30 - 4:30)Brain Parcellation (Glasser) PDF: Day1_Lecture3_Brain_Parcellation_Glasser.pdf
PPT: Day1_Lecture3_Brain_Parcellation_Glasser.pptx
Lecture 4 (4:30 - 5:30)rfMRI background, preprocessing, denoising (Smith) PDF: Day1_Lecture4_rfMRI_Preprocessing_Denoising_Smith

Day 2 (Tuesday, 9 June): Resting-state fMRI; network analysis

Type (Time)CourseResources
Lecture 5 (8:00 - 9:00)Resting State Analysis II (Burgess) PDF: Day2_Lecture5_rfMRI_Analysis_II_Burgess.pdf
PPT: Day2_Lecture5_rfMRI_Analysis_II_Burgess.pptx
Practical 3 (9:00 - 10:30)rfMRI Preprocessing, Denoising; ICA-based parcellations PDF: Day2_Practical3_rfMRI_processing&parcellation.pdf
Lecture 6 (11:00 - 12:00)rfMRI Network Analysis Strategies (Smith) PDF: Day2_Lecture6_rfMRI_Network_Analysis_Strategies_Smith.pdf
Practical 4 (1:30 - 3:30)rfMRI Netmats & Dual Regression PDF: Day2_Practical4_rfMRI_Netmats_Dual_Regression.pdf
Lecture 7 (3:30 - 4:30)Multimodal Classification of Areas in Individuals and Parcellation Validation (Glasser) PDF: Day2_Lecture7_Multi-modal_Classification_Glasser.pdf
PPT: Day2_Lecture7_Multi-modal_Classification_Glasser.pptx
Lecture 8 (4:30 - 5:30)Monitoring and Evaluating HCP Data Quality (Harms) PDF: Day2_Lecture8_HCP_QC_Harms.pdf

Day 3 (Wednesday, 10 June): Diffusion imaging and tractography; 7T acquisition and analysis

Type (Time)CourseResources
Lecture 9 (8:00 - 9:00)Diffusion MRI, Distortion Correction & DTI (Andersson) PDF: Day3_Lecture9_Diffusion_Andersson.pdf
Practical 5 (9:00 - 10:30) Diffusion MRI, Distortion Correction & DTI PDF: Day3_Practical5_dMRI&DTI.pdf
Lecture 10 (11:00 - 12:00)Fibre Orientation Models & Tractography Analysis (Bastiani) PDF: Day3_Lecture_10_Tractography_Bastiani.pdf
Practical 6 (1:30 - 3:30)Fibre Orientation Models & Tractography PDF: Day3_Practical6_Tractography.pdf
Lecture 11 (3:30 - 4:30)Regression, Prediction & Permutation Analyses (Nichols) PDF: Day3_Lecture_11_Modelling_Inference_Nichols.pdf
Lecture 12 (4:30 - 5:30)Family structure & Heritability (Nichols) PDF: Day3_Lecture_12_Family_Structure_Heritability_Nichols.pdf

Day 4 (Thursday, 11 June): Task-fMRI; data mining; disease connectomics

Type (Time)CourseResources
Lecture 13 (8:00 - 9:00)Task fMRI and Behavior Measures in HCP (Burgess/Harms) PDF: Day4_Lecture_13_tfMRI_Burgess.pdf
Practical 7 (9:00 - 10:30)Task fMRI Analyses PDF: Day4_Practical7_Task_fMRI.pdf
Lecture 14 (11:00 - 12:00)HCP Informatics: ConnectomeDB and Cloud-based Processing (Marcus) PDF: Day4_Lecture_14_HCP_Informatics_Marcus.pdf
Practical 8 (1:30 - 3:30)Cloud-based Processing using HCP Pipelines & Amazon Web Services PDF: Day4_Practical8_Cloud-Based_Processing.pdf
Lecture 15 (3:30 - 4:30)Understanding the Clinical Connectome: Application of HCP Methods to Neuropsychiatric Illness (Anticevic) PDF: Day4_Lecture_15_Clinical_Connectomics_Anticevic.pdf
Lecture 16 (4:30 - 5:30)Using 7T Multimodal Data (Xu) PDF: Day4_Lecture_16_Using_7T_Xu.pdf

Day 5 (Friday, 12 June): Magnetoencephalography; multimodal integration

Type (Time)CourseResources
Lecture 17 (8:00 - 9:00)Introduction to HCP-MEG Connectome (Larson-Prior) PDF: Day5_Lecture_17_Intro_HCP_MEG_Larson-Prior.pdf
Practical 9 (9:00 - 10:30)MEG preprocessing, channel & source analysis of tMEG and rMEG PDF: Day5_Practical9_MEG_I
Lecture 18 (11:00 - 12:00)Assessment of connectivity with MEG (Schoffelen) PDF: Day5_Lecture_18_MEG_Connectivity_Schoffelen
Practical 10 (1:30 - 3:30)rMEG and tMEG source-level connectivity; Multimodal Integration PDF: Day5_Practical_10_MEG_II.pdf
Lecture 19 (3:30 - 4:30)Follow-up analyses for HCP MEG data and other software tools (Oostenveld) PDF: Day5_Lecture_19_Followup_MEG_Analyses_Oostenveld.pdf
Lecture 20 (4:30 - 5:30)HCP: Looking back—and forward (Van Essen) PDF: Day5_Lecture_20_HCP_Course_Wrapup_VanEssen.pdf

On This Page:

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

We are pleased to announce the 2015 HCP Course: "Exploring the Human Connectome", to be held June 8-12 at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, 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 data from the Human Connectome Project using methods and informatics tools developed by the WU-Minn HCP consortium plus data made freely available to the neuroscience community. 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.

The 2015 FSL Course will also be run in the same venue on the same days. Because the two courses are totally separate and self-contained, it will not be logistically possible for attendees to attend sessions from both courses.

The HCP and FSL courses run the week before OHBM 2015 (June 14-18 at the Hawaii Convention Center in Honolulu).

If you require an invitation letter as part of a travel visa application, please download this letter and fill in your contact information.

Accommodation & Location Information

The course will take place at the Waikiki Beach Marriott Resort and Spa, Hawaii, USA.
You will need to organize your own accommodation for the course. A limited number of discounted rooms are available at the Marriott at this website. There are also many local hotels in Waikiki Beach.

If you would like to share accommodation with another attendee (of either the HCP or FSL Courses), you may enter your contact information on our publicly-viewable wiki page.  


Speakers: David Van Essen, Steve Smith, Jesper Andersson, Dan Marcus, Matt Glasser, Michael Harms, Greg Burgess, Tom Nichols, Matteo Bastiani, Alan Anticevic, Gordon Xu, Robert Oostenveld, Jan-Mathijs Schoffelen, Linda Larson-Prior

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

Cancellation Policy (Updated May 18, 2015)

Please book with care. We have made commitments on costs that cannot be changed this close to the course date, and can no longer offer full refunds on registration cancellations. We cannot offer refunds of any kind for any cancellation within two weeks of the event (from May 25th on). We can offer 50% refund on cancellations between now and then.

Contact Information

If you have any questions, please contact us at:

We look forward to seeing you in Hawai'i!