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.
Note: You can download all HCP Course materials en masse from wustl.box.com
Day 1 (Monday, 8 June): Structural imaging; preprocessing; intersubject registration; parcellation
Type (Time) | Course | Resources |
---|---|---|
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) | Course | Resources |
---|---|---|
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) | Course | Resources |
---|---|---|
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) | Course | Resources |
---|---|---|
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) | Course | Resources |
---|---|---|
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:
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.
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
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.
If you have any questions, please contact us at: hcpcourse@humanconnectome.org
We look forward to seeing you in Hawai'i!
Make sure you have at least 1TB of free disk space. The downloaded archive must be opened within VM virtualizer software software (VMware Player, VMware Fusion, or VirtualBox) where you will run the VM. If your internal storage has more than 1TB of space free, this will generally be acceptably fast for the purpose.
If you are planning to buy a new external drive for this purpose, we recommend that you check the computer(s) you intend to use it with for USB 3, eSATA, or Thunderbolt ports, and get an external drive with whichever of those interfaces your computer(s) have. USB 2 will work, but at significantly reduced performance speed.
This download requires the Aspera plugin and a free ConnectomeDB account. We recommend using Firefox to download as Aspera is not well supported in Chrome.
Remember to change the settings in the Aspera Connect plugin (via the “gear” icon in the Transfers window or through Aspera Connect Menu>Preferences>Transfers) to download to your desired location. The default in Aspera Connect is to download to your desktop (which you probably don’t want).
Make sure you have at least 1TB of free disk space to download and extract the data.
If you are planning to buy a new external drive for this purpose, we recommend that use one compatible with USB 3, eSATA, or Thunderbolt connections. USB 2 will work, but at significantly reduced performance speed.
This download requires the Aspera plugin and a free ConnectomeDB account.
Remember to change the settings in the Aspera Connect plugin (via the “gear” icon in the Transfers window or through Aspera Connect Menu>Preferences>Transfers) to download to your desired location.
The paths provided throughout the HCP Course practical instructions, both for locating the software to run and for locating the data to process, will very likely not be correct for your particular configuration of software and data. You will be responsible for keeping track of these paths (where you installed the software and where you placed the data) and altering the commands provided in the course materials to reflect your chosen configuration.
Additionally, the MEG practicals for Day 5 use precompiled MATLAB scripts that will only work on Linux systems. If you don’t have a Linux machine and want to run the MEG practicals, we recommend downloading the Course VM as in Option 1.
Requisite for running the HCP Pipelines: FreeSurfer version 5.3.0-HCP.
See this installation guidance for using the prerequisite software in the HCP pipelines.