This repository contains descriptions of, and links to, all projects created by participants at Neurohackademy 2019. If you're adding a new project, please use the template below.
- Project template: Template to use when creating new projects
When adding a new project to the listing, please copy and paste the template below.
Project url(s): [link to GitHub repo or other resources]
Contributors: [list of people involved], NAME
Description of project: [a few sentences describing the project]
How to get involved: [optional explanation of how one can get involved in the project]
Project url(s): https://github.com/matanmazor/BrainViz
Contributors: Anna Jafarpour, Matan Mazor, Liberty Hamilton.
Description of project: With BrainViz we can visualize neural activity in selected ECOG contacts.
How to get involved: Please get in touch with one of the contributors.
Project url(s): Neurohackmap github repo
Contributors: Antonija Kolobaric, Giacomo Ariani, Hannah Coyle, Johnny Lau, Daria Proklova, Damion V. Demeter
Description of project: Neurohackmap is a collection of scripts to visualize the change in NHA19 participants' world locations and research interests over time.
How to get involved: For any help in code optimization, and/or to add alternative data visualizations, pull requests are welcome. Please get in touch with one of the contributors if you would like to request full access to the dataset.
Project url(s): neurohack_dl_gan
Contributors: Meltem Atay, Bastian David, Jeffrey Durieux, Alberto Lazari, Steph Rossi, Anna Truzzi, Benjamin Wade, Suniyya A. Waraich
Description of project: We are working on classifying a person's age group from an MRI scan, using deep learning techniques. At the same time, we are training a GAN that takes in young brains and makes them look old. 🧠
How to get involved: Say hi! 👋 Leave a note.
Project url(s): Volume to HCP surface,
GIFTI API proposal
Contributors: Hao-Ting Wang (HCP, visualisation, GIFTI),
Gia H Ngo (HCP, visualisation),
Chris Markiewicz (GIFTI)
Description of project: We want to put our preprocessed volume space data on to the HCP surface template. The goal is to have the whole workflow in Python. Due to the lack of high-level surface-based tools, we are also looking into solutions to GIFTI/CIFTI file IO and visualisation. The future goal is to provide more user-friendly tools to work with surface data in Python!
How to get involved: You discuss the new GIFTI API under issues or help Gia withe the python workflow.
Project url(s): Neuropythy for Dev GitHub Repo
Contributors: Maya Rosen, Kendra Seaman, Aarti Nair, Megan McMahon, Leehyun Yoon, Noah Benson
Description of project: Use neuropythy to visualize developmental changes in brain structure in participants from the HCP Lifespan Pilot Study.
Goals: 1) Access and download HCP Lifespan Pilot Data, 2) Run HCP preprocessing pipelines using a docker container on AWS, 3) Use neuropythy to retrieve and visualize age-related differences in structural properties like cortical thickness.
How to get involved: Suggestions for other types of structural analysis (gyrification, TI/T2 differences) and functional analysis (resting state, tasks) are welcome. We look forward to analyzing the HCP-D and HCP-A datasets in the near future!
Project url(s): natstim_neurohack
Contributors: Jacob Fischer,
Mai Lin Nguyen, Marissa Clark,
Sam Nastase, Adina Wagner
Description of project: How accurate and variable are annotations provided by various tools
for automated feature extractions?
We try to use available interfaces in pliers for face and speech annotation
on the movie Forrest Gump, and aim to evaluate their results accuracy and variance.
How to get involved: Find us in the common area!
Project url(s): github repo
Contributors (in alphabetical order of last names): Katie Bottenhorn, Bharath Chandra Talluri, Julio A Yanes
Description of project: Use activation maps of four different tasks from various studies obtained through Brainmap, and Neurosynth and train a classifier to predict the task from an activation map.
How to get involved: We look forward to scaling this project to different tasks, and ideally towards more general applications.
Project url(s): github repo
Contributors (in alphabetical order of last names):Elizabeth Beard, Stephanie DeCross, Damion Demeter, Chris Foulon, Sofia Fernandez-Lozano, Helena Gellersen, Ayelet Gertovski, Estee Rubien-Thomas, Saren Seeley, Catherine Walsh
Description of project: Provide context for the image quality metrics (IQMs) shown in the MRIQC group reports, by showing the distribution of IQMs for your data plotted relative to a larger set of anonymized IQMs pulled from the web API.
How to get involved: We're looking forward to expanding this project, see our contributing page for more info on how to contribute.\
Project url(s): https://github.com/DanNBullock/NeuroAnatParse
Contributors: Daniel Bullock, Johnathan Avery
Description of project: TractFunc is an initial attempt to probe the (potential) functional roles of white matter tracts. Repo also includes code for text corpus parsing specific to white-matter anatomy literature
How to get involved: Join in the project?
Project url(s): github repo
Contributors (in alphabetical order of last names): Azeez Adebimpe, Ryan Timms, Martina G. Vilas
Description of project: We will simulate MEG source data with deep sources activations (e.g. hippocampal activity) to estimate which source reconstruction method is more efficient in these cases. For a detailed overview of our project, see our project-outline.
How to get involved: You can find the next steps of our project in our README. You can also scroll around our jupyter-notebooks and add/change anything in them by submitting a pull request.
Project url(s): PyCortexEdu GitHub repo
Contributors: Paul Scotti, Arman Kulkarni, Matan Mazor, Eduard Klapwijk, Alex Huth
Description of project: In-browser 3D brain visualization of different brain atlases, parcellations and associated terms and variance components of the neuroimaging literature from Neurosynth. This can be used as educational resource and potentially for researchers to evaluate functional and structural probabilities of selected brain regions. The PyCortex software library is used for visualisation.
How to get involved: Click around that brain and send us some pull requests!
Project url(s): gitHub repo
Contributors: Carol Jew, Gerson Guercio, Lindsay Oliver, Sarah Lichenstein, Teddy Turesky
Description of project: We are attempting to predict substance use using behavioral metrics from the HCP data with machine learning models. Many measures relate to substance use, but there’s little data available to guide the development of test batteries. The goal is to minimize patient burden without sacrificing predictive accuracy.
How to get involved: Feel free to get in touch with one of the contributors or send us pull requests.
Project url(s): https://github.com/KulikovaSofya/BrainStim
Contributors: Sofya Kulikova, Daniel Bullock
Description of project: With this python script you can estimate effects of TMS for a particular white matter fiber reconstructed from diffusion MRI data. Input data: T1-w image, FA map, reconstructed fibers in trk .format, estimated e-field in a mesh format. Output: estsimated stimulations effects at each point of the provided fibers
How to get involved: There is a number of points that should be improve including 1) building a Docker container for this project; 2) improving registration between TMS and diffusion MRI; 3) Adding a function that would run e-field calculations within a program (to calculate e-field in place and not to take it as an input); 4) making things work faster (yes, it's very slow now); 5) still problems with visualization. Please, feel free to contact if you would like to contribute to this project.