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
| Type | Course (Presenter) | Resources |
|---|---|---|
| Welcome | Intro and Overview (David Van Essen) | PDF: https://wustl.box.com/s/0edcj787ye9c2idc2ir95b766w8r3pqz |
| Lecture | HCP Data Acquisition (Michael Harms) | PDF: https://wustl.box.com/s/sp4bcf9wjaao6lj3ysmlh495rjds9qsv |
| Practical | Introduction to wb_view (Jenn Elam) | PDF: https://wustl.box.com/s/ndirdpom847h0f0ozrqleibxv9w4ssdw |
| Lecture | Structural MRI: Precise Neuroanatomical Localization (Matt Glasser) | PDF: https://wustl.box.com/s/d8rrs4cyhbbuoptvjywe1uqhpn3kd9fv |
| Lecture | Data Quality (Michael Harms) | PDF: https://wustl.box.com/s/72nudch8z8bponfmyvfaxj0421zc18fo |
| Practical | Data Quality (Michael Harms) | PDF: https://wustl.box.com/s/0gpam933mvrstcoitm3yfl4p26n85gl2 |
| Lecture | Group Brain Parcellation (Matt Glasser) | PDF: https://wustl.box.com/s/eyot0msmq58kpaod785z3qqhgejk3oif |
| Practical | Introduction to wb_command and Group Parcellation (Tim Coalson, Jenn Elam) | PDF: https://wustl.box.com/s/k4ptm6mrxar1nlfwhzarmihsv5qwd970 |
Day 2: Monday, Aug 29
| Type | Course (Presenter) | Resources |
|---|---|---|
| Lecture | Multimodal Classification of Areas in Individuals and Parcellation Validation (Matt Glasser) | PDF: https://wustl.box.com/s/i2mxsxjt6ac9d5xuqjct49hjnve75ck5 |
| Practical | Individual Brain Parcellation (Matt Glasser) | PDF: https://wustl.box.com/s/0ln9dtwouzhqxkuw5nh7x3bnr5tlsnjh |
| Lecture | rfMRI background, Preprocessing, Denoising (Steve Smith) | PDF: https://wustl.box.com/s/4mo9frrozy5oprsdah7jecfvplkm3wiq |
| Lecture | rfMRI Temporal Noise (Steve Smith, Matt Glasser) | PDF: https://wustl.box.com/s/jbqr6k3oy4o92nxa62vonk0nhglce2ue |
| Practical | rfMRI Preprocessing, Denoising; ICA-based Parcellations (Steve Smith) | PDF: https://wustl.box.com/s/xl5oq5pvtg0v1jd719uygw4xdzp31y9t |
| Lecture | rfMRI Network Analysis Strategies (Steve Smith) | PDF: https://wustl.box.com/s/kxzlemlbosyn75pn61cpbxgbcypv49zn |
| Practical | rfMRI Netmats and Dual Regression (Steve Smith) | PDF: https://wustl.box.com/s/se8fwaocighr3libgerd9uh34xvywtd6 |
Day 3: Tuesday, Aug 30
| Type | Course (Presenter) | Resources |
|---|---|---|
| Lecture | HCP Pipelines (Tim Brown) | PDF: https://wustl.box.com/s/9ds0jaxliwebeoxqdvxel86x7g6z4sul |
| Practical | HCP Pipelines Practical (Tim Brown) | PDF: https://wustl.box.com/s/4u30jlz6cmsekpw2sxbcfq0wc33nze37 |
| Lecture | Regression, Prediction, and Permutation Analyses (Thomas Nichols, Anderson Winkler) | PDF: https://wustl.box.com/s/z8ienimugue86kvans6ks421v9ycmay2 |
| Lecture | Family Structure and Heritability (Thomas Nichols) | PDF: https://wustl.box.com/s/lsab6irc5k2q1jrgrp0beiuo67v0y4hw |
| Lecture | Task fMRI and Behavioral Measure Analyses (Greg Burgess) | PDF: https://wustl.box.com/s/tbkv3u299zqupgsgzk402waqo3nw83ah |
| Practical | tfMRI and PALM (Greg Burgess, Anderson Winkler) | PDF: https://wustl.box.com/s/0xqeqhf84fuenmykjdfxbrydawpryn6v |
| Lecture | HCP Informatics (Daniel Marcus) | PDF: https://wustl.box.com/s/9xmofvj0nyjox7xp136j9joes1hbhn96 |
| Lecture | Understanding the Clinical Connectome: Application of HCP Methods to Neuropsychiatric Illness (Alan Anticevic) | PDF: https://wustl.box.com/s/kfvzywxr9pt4dqerc4i3bqep6oluzsqu |
Day 4: Wednesday, Aug 31
| Type | Course (Presenter) | Resources |
|---|---|---|
| Lecture | Diffusion MRI, Distortion Correction and DTI (Jesper Andersson) | PDF: https://wustl.box.com/s/lpor0s3vt2qwaghwfaj4ed6hr8lwhnqu |
| Practical | Diffusion MRI, Distortion Correction and DTI Practical (Jesper Andersson) | PDF: https://wustl.box.com/s/2m0ix0zkia16vb7a58agidiufq6g4ag6 |
| Lecture | Fibre Orientation Models and Tractoghraphy Analysis (Michiel Cottar) | PDF: https://wustl.box.com/s/pzbdltem3jxjs0uxhz51p3mfpd9csdt5 |
| Practical | Fibre Orientation Models and Tractography Analysis Practical (Michiel Cottar) | PDF: https://wustl.box.com/s/35m28use7mv9lsdt3ixbqx4zp0fi4sgm |
| Practical | Tractography and Tracer (Chad Donahue) | PDF: https://wustl.box.com/s/ovp9ev6h2wcsykc2kni4x9rshaet6fuq |
| Lecture | Cloud-based Processing (Daniel Marcus) | PDF: https://wustl.box.com/s/f08yp2k1o4ijyocpw1h4c9xlknhq2t07 |
| Practical | Cloud-based Processing Using HCP Pipelines and Amazon Web Services (Tim Brown) | PDF: https://wustl.box.com/s/xocq331xo761pnmj8kkbohwo21t6cchv |
Day 5: Thursday, Sep 1
| Type | Course (Presenter) | Resources |
|---|---|---|
| Lecture | Introduction to HCP-MEG Connectome (Linda Larson-Prior) | PDF: https://wustl.box.com/s/baxn8g12s0qi0h9ju84typyocnk36u1x |
| Practical | MEG Preprocessing, Channel and Source Analysis of tMEG and rMEG (Giorgios Michalareas, Franceso di Pompeo) | PDF: https://wustl.box.com/s/1i5jhm94y9lsl9hby46085j3qbtajozy |
| Lecture | MEG Connectivity and Follow-up Analyses for HCP MEG Data and Other Software Tools (Robert Oostenveld) | PDF: https://wustl.box.com/s/8ijsz9gahqf4g21cm0yrp2x98va4cn4v |
| Practical | rMEG and tMEG Source-level Connectivity; Multimodal Integration (Giorgios Michalareas, Franceso di Pompeo) | PDF: https://wustl.box.com/s/39h0dcq63g7qy9erx4s2nk3e52nmiqw8 |
| Practical | Building wb_view scenes and sharing on BALSA (Jenn Elam) | PDF: https://wustl.box.com/s/6nv4ezqrcpsj86vtyx1ttotdet9p6yb3 |
| Lecture | HCP and Beyond: Looking Back and Forward (David Van Essen) | PDF: https://wustl.box.com/s/0tc4qef30czwhbc7tgh10qeisw7rj51m |
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.
Faculty
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: hcpcourse@humanconnectome.org
We look forward to seeing you in Bah-ston!
Before you download the Course VM...
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).
Before you download the Practical Data…
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.
Prerequisite software for running the 2015 HCP Course Practicals
- FSL version 5.0.6
- Connectome Workbench v1.1.1
- megconnectome v2.2 and fieldtrip-r9924
- MATLAB with the official MATLAB toolboxes: Statistics, Bioinformatics, and Signal Processing OR Octave v.3.8.0 or greater with toolboxes: control, general, signal, and statistics
- HCP Pipeline Scripts v3.4.0
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.