Archived Neurohackademy Lectures

Welcome to NeuroHackademy!

Noah C. Benson, Ariel Rokem

Coffee break

Reproducibility in cognitive neuroscience: What is the problem?

Russell Poldrack

Lunch

Big Data, Small Data: Considerations for Modeling and Inference in Neuroimaging

John Van Horn

Coffee break

Studying human functional brain networks: two paths to reliability

Caterina Gratton

Opening reception and dinner

AI-assisted programming

Russell Poldrack

Coffee break

Introduction to programming in Python

Kelly Chang

Scientific computing in Python

Noah C. Benson

Designing and implementing Python libraries

Ariel Rokem

Lunch

Introduction to version control with git and GitHub

John Kruper

Collaboration patterns with git and GitHub

Ariel Rokem

Coffee break

Introduction to machine learning (scikit learn)

Ariel Rokem

Introduction to deep learning (pytorch)

Noah C. Benson

Hands on group projects

Noah C. Benson

Coffee break

Overview of a diffusion imaging pipeline using DIPY

Serge Koudoro

Lunch

Processing neuroimaging data : analytical flexibility curse and blessing and the Nipoppy proposal

J. B. Poline

Coffee break

Hands on group projects

Ariel Rokem, Noah C. Benson

Center for Human Neuroscience visit

John Pyles

Building a Brain Map: Ethical Issues on the Frontier of Neuroscience

Timothy Brown

Coffee break

Principles of science communication: visualization, writing, and speaking

Kendrick Kay

Lunch

User-friendly web apps to facilitate fMRI design and analysis

Stephanie Noble

Coffee break

Panel discussion: careers in neuroimaging and data science

Pizza night

Dataset showcase

Noah C. Benson, Ariel Rokem

Coffee break

Nilearn for statistical analysis and machine learning in fMRI

Elizabeth DuPre

Lunch

Hands on group projects

Ariel Rokem, Noah C. Benson

Coffee break

GitHub Actions: The Scientist’s Automation Toolkit

Serge Koudoro

Quality assessment and control of unprocessed anatomical, functional, and diffusion MRI of the human brain using MRIQC

McKenzie Hagen

Introduction to cloud computing

Naomi Alterman

Hack pitches

Coffee break

Lunch

Coffee break

GitHub workflow for project management

Anshul Tambay

Coffee break

Lunch

Coffee break

Coffee break

Lunch

Lightning talks

Coffee break

Coffee break

Lunch

Coffee break

Coffee break

Lunch

Project presentations

Coffee break

Project presentations

Welcome to NeuroHackademy!

Noah C. Benson, Ariel Rokem

Coffee break

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Lunch

Bringing the Brain into Focus through a Science of Data

John Van Horn

Coffee break

Coffee break

Unleashing the Krakencoder: a multi-modal connectome mapping and fusion tool

Amy Kuceyeski

Welcome reception

AI-assisted coding

Russell Poldrack

Coffee break

Designing and implementing Python libraries

Ariel Rokem

Introduction to programming in Python

Kelly Chang

Lunch

Introduction to version control with git

Noah C. Benson

Collaboration patterns with git and GitHub

Ariel Rokem

Coffee break

Coffee break

Reproducibility and the future of qMRI research

Nikola Stikov

Responsible Data Governance for Neuroscience: the role of ethics and the law

Damian Eke

Coffee break

Data visualization in Python

Kelly Chang

Docker

Noah C. Benson

Lunch

Introduction to machine learning

Ariel Rokem

Introduction to deep learning

Noah C. Benson

Coffee break

Coffee break

Cloud computing

Naomi Alterman

Distributed data sharing

J. B. Poline

Canonical response parameterization of event-locked timeseries data and clustering with basis profile curves

Kai Miller

Coffee break

Introduction to imaging genetics

Jennifer Forsyth

Lunch

Statistical and sociological components of reproducibility

J. B. Poline

Coffee break

Coffee break

Panel discussion: careers in neuroimaging and data science

Working with multimodal data in the Brain Imaging Data Structure

Dora Hermes

Coffee break

Dataset showcase

Noah C. Benson, Ariel Rokem

Lunch

User-friendly web apps to facilitate fMRI study design and analysis

Stephanie Noble

Coffee break

Coffee break

Review sessions

Noah C. Benson, Kelly Chang, Ariel Rokem

GitHub for Project Management

Anshul Tambay

Coffee break

Hack project pitches

Lunch

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Lightning talks

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Coffee break

Coffee break

Breakout sessions

Coffee break

Lunch

Coffee break

Coffee break

Final presentations

Farewell reception

Introduction to NeuroHackademy

Ariel Rokem, Noah C. Benson

Coffee break

Introduction to Python

Kelly Chang

Advanced programming in Python

John Kruper

Lunch

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Coffee break

Coffee break

Measuring and analyzing human functional brain networks

Caterina Gratton

Welcome reception

Introduction to Python

Kelly Chang

Advanced programming in Python

John Kruper

Coffee break

Building web applications

Adam Richie-Halford

Building software libraries in Python

Ariel Rokem

Lunch

Introduction to version control with git

Noah C. Benson

Collaboration patterns with git/GitHub

Ariel Rokem

Coffee break

Coffee break

AI-assisted programming

Russell Poldrack

Responsible Data Governance for Neuroscience: the role of ethics and the law

Damian Eke

Coffee break

Software containerization with Docker

Noah C. Benson

Data visualization in Python

Kelly Chang

Lunch

Contributing to large-scale international neuroimaging initiatives through coordinated data analysis

Neda Jahanshad

Coffee break

Coffee break

Cloud computing

Naomi Alterman

Introduction to Machine Learning

Ariel Rokem

BIDS-iEEG in practice to map electrical stimulation driven connectivity

Dora Hermes

Coffee break

Machine learning methods for neuroimaging

Elizabeth DuPre

Lunch

Statistical and sociological components of reproducibility

J. B. Poline

Coffee break

Coffee break

Careers in neuroimaging and data science

Networking event

Processing intracranial data with MNE-python

Liberty Hamilton

Coffee break

The Brain Imaging Data Structure

Ariel Rokem

Introduction to deep learning

Noah C. Benson

Lunch

Data showcase

Ariel Rokem, Noah C. Benson

Coffee break

Coffee break

Review sessions

Ariel Rokem, John Kruper

Review sessions

Noah C. Benson, Kelly Chang

Neural decoding in the wild

Bing Brunton

Coffee break

Software development project management

Vani Mandava

Lunch

Hackathon pitches

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Lightning talks

Coffee break

Coffee break

Breakout sessions

Morning standup

Coffee break

Lunch

Coffee break

Coffee break

Breakout sessions

Coffee break

Lunch

Coffee break

Coffee break

Final presentations

Farewell reception

Welcome to NeuroHackademy

Ariel Rokem, Noah C. Benson

Icebreaker

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Lunch

What if all the data in the world were instantly accessible?

Satra Ghosh

Coffee Break

Coffee break

Neural decoding in the wild

Bing Brunton

Welcome reception

Introduction to Python: the Basics

Noah C. Benson

Data management in Python/Pandas

Ariel Rokem

Coffee break

Meta-analysis and reproducibility

Angela Laird

Lunch

Git from Scratch

Noah C. Benson

Collaboration patterns with Git

Ariel Rokem

Coffee Break

Coffee break

Docker

Noah C. Benson

Poster session

Data visualization in Python

Ariel Rokem

Introduction to Python: Control Flow

Noah C. Benson

Coffee break

Responsible data governance for neuroscience: the need for FAIR-C

Damian Eke

Lunch

Measuring and analyzing human functional brain networks

Caterina Gratton

Coffee Break

Coffee break

Hands on meta-analysis / NIMARE

Taylor Salo

Introduction to machine learning / scikit learn

Ariel Rokem

Parallelization with Python/Dask

Ariel Rokem

Introduction to Python: NumPy

Noah C. Benson

Coffee break

BIDS-iEEG in practice to map electrical stimulation driven connectivity

Dora Hermes

Lunch

Data management for neuroimaging with datalad

Adina Wagner

Coffee Break

Coffee break

Cloud computing

Naomi Alterman

Deep learning

Noah C. Benson

Processing intracranial data with MNE-python

Liberty Hamilton

Coffee break

The issues with statistics that will make your work irreproducible – and what we should do about it

J. B. Poline

Lunch

Data showcase

Melanie Ganz, Kendrick Kay, Adam Richie-Halford, Noah C. Benson

Coffee Break

Coffee break

Review session 1

Noah C. Benson

Review session 2

Ariel Rokem

Hackathon pitch session

Coffee break

Hacking

Lunch

Hacking

Coffee Break

Coffee break

Morning standup

Coffee break

Hacking

Lunch

Lightning talks

Coffee Break

Coffee break

Breakout session

Ariel Rokem

Breakout session

Kendrick Kay

Morning standup

Coffee break

Hacking

Lunch

Careers in data science and neuroimaging (panel)

Coffee Break

Coffee break

Breakout session

Ariel Rokem

Breakout session

Noah C. Benson

Morning standup

Coffee break

Hacking

Lunch

Hacking

Coffee Break

Coffee break

Morning standup

Coffee break

Hacking

Lunch

Hack presentations

Coffee Break

Coffee break

Farewell event

Welcome!

Ariel Rokem, Noah C. Benson

Get-to-know-ya

Introduction to programming in Python

Noah C. Benson

Cloud computing

Tara Madhyastha, Ariel Rokem, Andrew Crabb

Coffee break

Morning check in

Diffusion Imaging in Python

Eleftherios Garyfallidis

Advanced programming in Python

Noah C. Benson

Using git and GitHub for collaboration

Ariel Rokem

Meta-analysis and reproducibility

Angela Laird, Taylor Salo

Coffee break

Morning check in

Developing Open Source Software for science: a case study of PsychoPy

Jon Peirce

Neuroimaging in Python Q&A

Satra Ghosh, Elizabeth DuPre

Machine learning in Python

Ariel Rokem

Docker

Noah C. Benson

Coffee break

Morning check in

Responsible data governance for Neuroscience

Damian Eke

Measuring and analyzing human functional brain networks

Caterina Gratton

Using git and GitHub for collaboration

Ariel Rokem

Docker

Noah C. Benson

Self-supervised approaches for neural decoding and alignment

Eva Dyer

Coffee break

Morning check in

Pytorch

Noah C. Benson

Data visualization in Python

Ariel Rokem

The issues with statistics that will make your work irreproducible – and what we should do about it

J. B. Poline

Extending the Brain Imaging Data Structure to intracranial EEG

Dora Hermes

Careers in neuroimaging and data science

Anisha Keshavan, Teon Brooks, Chris Gorgolewski, Tal Yarkoni

Coffee break

Morning check in

Resource showcase

Hackathon pitches

Hacking

Coffee break

Stand up meeting

Lightning talks

Hacking

Coffee break

Stand up meeting

Lightning talks

Hacking

Coffee break

Stand up meeting

Fireside chat

Russell Poldrack

Hacking

Karaoke!

Coffee break

Stand up meeting

Hacking

Hack project presentations

Coffee break

Introduction to NeuroHackademy

Ariel Rokem, Tal Yarkoni

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Ethical considerations in neuroimaging data science and beyond

Tal Yarkoni

Ice-breaker

Introduction to programming in Python

Tal Yarkoni

High-performance Python

Ariel Rokem

From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends.

Fernando Perez

Coffee break

Version control with git/GitHub

Elizabeth DuPre

Docker

Chris Gorgolewski

Data manipulation in Python (Numpy/Pandas)

Tal Yarkoni

Creating share-able Python libraries

Ariel Rokem

Introduction to Machine Learning

Tal Yarkoni

Data visualization in Python

Kirstie Whitaker

Meta-analysis and reproducibility

Angela Laird

The difference between prediction and explanation

Jeanette Mumford

Coffee break

Workflows/Nipype

Satra Ghosh

NiBabel: Neuroimaging data and file structures in Python

Chris Markiewicz

Nilearn

Elizabeth DuPre

Nipreps

Oscar Esteban

Brain Imaging Data Structure (BIDS)

Kirstie Whitaker

High Stakes Neuroimaging: A transition to translational medicine in industry

Anisha Keshavan

Visualizing invasive and non-invasive EEG data

Liberty Hamilton

Introduction to the Geometry and Structure of the Human Brain

Noah C. Benson

Word embeddings as priors for language encoding models

Alex Huth

Reproducibility: what you need to know from epistemology to statistics

J. B. Poline

Coffee break

Machine learning for neuroimaging

Gael Varoquaux

Functional brain parcellation

Pierre Bellec

Cloud computing for neuroimaging

Tara Madhyastha, Amanda Tan, Ariel Rokem

Panel discussion: neuroimaging and data science careers

Chris Gorgolewski, Anisha Keshavan, Chris Chatham

Testing and accounting for confounding variables

Manjari Narayan

Optimization (ADSI)

Sasha Aravkin, Prasanna Raut, Kelsey Maass, Maryam Fazel

Optimal transport (ADSI)

Zaid Harchaoui, Lang Liu

Panel discussion: Python ecosystem Q&A

Tal Yarkoni, Satra Ghosh, Noah C. Benson, Chris Markiewicz

Coffee break

Brain hacking 101

Ariel Rokem, Tal Yarkoni

Coffee break

Coffee break

Coffee break

Coffee break

Coffee break

Coffee break

Breakfast

Introduction to NeuroHackademy

Ariel Rokem, Tal Yarkoni

Coffee break

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Lunch

The FAIR principles

Maryann Martone

Collaborating with git and GitHub

Elizabeth DuPre

Docker

Anisha Keshavan

Coffee break

Coffee break

Office hours

Welcome reception + dinner

Breakfast

Plumbing the Intertubes: A Hitchhiker’s Guide to Information Filtering

Satra Ghosh

Introduction to Python

Tal Yarkoni

Building Python libraries

Ariel Rokem

Coffee break

Lunch

Numerical computing in Python

J. B. Poline

High-performance Python

Ariel Rokem

Coffee break

Data visualization

Kirstie Whitaker

Browser-based visualization with Javascript

Anisha Keshavan

Coffee break

Model-based fMRI and HCP data

Noah C. Benson

Office hours

Poster session

Breakfast

Measuring human functional brain networks

Caterina Gratton

Functional brain parcellation

Pierre Bellec

Coffee break

Neuroethics

Blaise Agüera y Arcas

Lunch

Machine learning with Scikit Learn

Tal Yarkoni

Coffee break

Coffee break

BIDS

Kirstie Whitaker

Jupyterlab and Binder

Elizabeth DuPre

Office hours

Breakfast

Open datasets for Neurohacking

Chris Gorgolewski

Coffee break

Meta-analysis and reproducibility

Angela Laird

Lunch

Optimization (ADSI)

Sasha Aravkin

Docker

Chris Gorgolewski

Coffee break

Optimization (ADSI)

Sasha Aravkin, Peng Zheng

Cloud computing

Amanda Tan, Ariel Rokem

Coffee break

Office hours

Breakfast

The difference between prediction and explanation

Jeanette Mumford

Evil p values

J. B. Poline

Coffee break

Finding low-dimensional structure in large-scale neural recordings

Eva Dyer

Lunch

Nipype

Satra Ghosh

Optimal transport (ADSI)

Zaid Harchaoui

Coffee break

Deep learning

Ariel Rokem

Optimal transport (ADSI)

Zaid Harchaoui

Coffee break

Office hours

Breakfast

Project pitches

Coffee break

Team formation and project scoping

Lunch

Hack session

Coffee break

Hack session

Coffee break

Breakout sessions

Breakfast

Hack session

Coffee break

Hack session

Lunch

Hack session

Coffee break

Hack session

Coffee break

Breakout sessions

Breakfast

Hack session

Coffee break

Hack session

Lunch

Hack session

Coffee break

Hack session

Coffee break

Breakout sessions

Breakfast

Hack session

Coffee break

Hack session

Lunch

Hack session

Coffee break

Hack session

Coffee break

Breakout sessions

Breakfast

Hack session

Coffee break

Presentation preparation

Lunch

Project presentations

Coffee break

Project presentations (continued)

Coffee break

Farewell party

Breakfast

Introduction to Neurohackweek

Ariel Rokem

Morning coffee

Reproducibility in fMRI: What is the problem?

Russell Poldrack

Lunch

Git/Github

Bernease Herman

Docker for scientists

Chris Gorgolewski

Introduction to Python

Tal Yarkoni

Introduction to R

Valentina Staneva

Afternoon coffee

Coffee break

Software testing

Chris Gorgolewski

Science: open for all

Kirstie Whitaker

Welcome Reception

Breakfast

From interactive exploration to reproducible data science: Jupyter, Binder, Travis and friends.

Fernando Perez

Morning coffee

Lunch

Numerical computing for neuroimaging

J. B. Poline

Python packaging

Ariel Rokem

Data visualization

Tal Yarkoni

Computer Vision

Michael Beyeler

Afternoon coffee

Coffee break

Data manipulation in Python/Pandas

Tal Yarkoni

High-performance Python

Ariel Rokem

Deep learning with Keras

Ariel Rokem

Poster session

Breakfast

Deep learning with Keras (part 2)

Ariel Rokem

Morning coffee

Neuroethics

Eran Klein

Lunch

Machine learning with scikit-learn

Jake Vanderplas

Afternoon coffee

Coffee break

The Brain Imaging Data Structure (BIDS)

Chris Gorgolewski

Introduction to web technologies

Anisha Keshavan

CRN resources

Chris Gorgolewski

Breakfast

Cloud Computing for Neuroimaging

Amanda Tan, Ariel Rokem

Morning coffee

Lunch

Panel discussion: fostering open communities

Chris Gorgolewski, Fernando Perez, Kirstie Whitaker, Gael Varoquaux, Satra Ghosh

Afternoon coffee

Software pipelines for reproducible neuroimaging

Satra Ghosh, Chris Gorgolewski

Coffee break

Breakfast

Predictive models using object-oriented, interactive analysis in Matlab: Tools and application to pain

Tor Wager

Morning coffee

Lunch

Finding low-dimensional structure in large-scale neural recordings

Eva Dyer

Afternoon coffee

AllenSDK and the Allen Brain Observatory

Nicholas Cain, Justin Kiggins

Coffee break

P-values and reproducibility issues

J. B. Poline

Breakfast

Machine learning in neuroimaging

Gael Varoquaux

Morning coffee

Lunch

R for statistical analysis of fMRI data

Tara Madhyastha

Afternoon coffee

Synthesizing fMRI using generative adversarial networks: cognitive neuroscience applications, promises and pitfalls

Sanmi Koyejo

Coffee break

Brain hacking

Cameron Craddock

Breakfast

Project pitches

Morning coffee

Lunch

Hackathon

Afternoon coffee

Coffee break

Breakfast

Hackathon

Morning coffee

Lunch

Hackathon

Afternoon coffee

Coffee break

Unconference session

Breakfast

Hackathon

Morning coffee

Lunch

Hackathon

Afternoon coffee

Allen Institute Office Hours

Justin Kiggins, Nicholas Cain

Coffee break

Unconference session

Breakfast

Hackathon

Morning coffee

Lunch

Project presentations

Afternoon coffee

Coffee break

Farewell party (Lake Union cruise)

Introduction to Neurohackweek

Ariel Rokem