config.yaml

# yaml-language-server: $schema=public/schemas/brainhack-config.json
event:
  year: 2025
  startDate:
    day: 26
    month: 3
    year: 2025
  endDate:
    day: 28
    month: 3
    year: 2025
displaySections:
  tutorial: true
  schedule: true
  twitterFeed: false
twitterUrl: https://twitter.com/uwobrainhack
faq:
  - question: What is a "Brainhack"?
    answer: |
      Brainhack is an academically and open science oriented hackathon which connects researchers
      from across many different disciplines to work together on innovative
      projects related to neuroscience. For more details and examples of past
      Brainhack projects click
      [here](https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0121-x).
  - question: Who can participate?
    answer: |
      Any students (undergraduate/graduate), post-docs, staff, faculty, or
      clinicians with an interest in coding, neuroscience or neuroimaging are
      encouraged to participate.
  - question: Will the event be in-person or virtual?
    answer: |
      Brainhack Western 2025 will be in-person.
  - question: |
      I am interested in attending a specific tutorial in-person. How do I do
      that?
    answer: |
      You will have the opportunity to build a schedule during registration by
      specifying which tutorials you wish to attend.  You should be able
      to attend any tutorials you wish.
  - question: What does registration include?
    answer: |
      In-person registration includes access to all in-person tutorials and the
      ability to join an in-person hacking project group. In-person registration
      also includes breakfast, lunch, and snacks on all three days.
  - question: Do I need to register if I only want to hack?
    answer: |
      Yes! Anyone wishing to participate in any aspect of Brainhack Western
      2023, even just hacking, needs to register.
  - question: How much does it cost?
    answer: The cost of the event is $5 CAD!
  - question: |
      Is it possible to attend if I am not affiliated with Western University?
    answer: |
      We are able to accommodate non-Western University affiliated attendees.
      Please note that all attendees will need to follow Western University
      COVID-19 campus rules.  Note that Brainhack Western
      does not offer travel stipends. Attendees traveling to London, ON are
      wholly responsible for their own travel, lodging, and any meals not
      already included with registration.
  - question: Will there be food?
    answer: |
      Yes! Breakfast, lunch, snacks, non-alcoholic
      beverages, and coffee will be provided throughout the event. Please
      indicate any dietary restrictions when you register. Also, to cut down on
      waste, please bring your own coffee mug and/or water bottle.
  - question: What should I bring?
    answer: |
      Please bring your own laptop, cables, chargers, USB sticks, and some form
      of identification (e.g. Student card or Driver's licence). Also bring
      anything else you may need to work on your project (hardware, datasets
      etc.).
  - question: What if I don't know how to code?
    answer: |
      Learning is an important component of a Brainhack. There will be tutorials
      and experts around to answer questions.
  - question: What if I can't attend all three days?
    answer: |
      You are welcome to attend as much or as little as your schedule allows.
      We understand that Brainhack Western 2025 is scheduled during a busy part
      of the academic year, so we have tried to scheduled breaks each day to
      give attendees time to decompress and attend to their own work.
forms:
  registration:
    type: cognito
    title: Brainhack 2025 Registration
    shortTitle: Registration
    embedTag: <script src="https://www.cognitoforms.com/f/seamless.js" data-key="dKVrRkF3yk6PnoRpFF7XGg" data-form="6"></script>
    prefillMappings:
      id: Calculations.VolunteerCode
registration:
  cost: 5
  url: /forms/registration
  # This can be uncommented to allow users to enter email addresses.
  # It should be a webhook that accepts the email as a simple json document with a
  # single "email" key.
  # In the past, I've used a make webhook to punt the email addresses on to a
  # google docs form.
  # Unless the dev is really committed however, it's probably not worth enabling this.
  # Hardly anyone signed up for the email list, and those same individuals were students
  # who would have got the registration email blast anyway.
  # emailSignupTarget: https://hook.us1.make.com/hrdtv28jy9i55havi84l6db2xc1ieyol
  openDate:
    day: 19
    month: 1
    year: 2025
  closeDate:
    day: 19
    month: 3
    year: 2025
  projectPitchUrl: https://github.com/BrainhackWestern/BrainhackWestern.github.io/issues/new?assignees=&labels=pitch&projects=&template=project-pitch.yml&title=%5BPitch%5D%3A+
location:
  name: Western Interdisciplinary Research Building
  street: Perth Dr
  city: London
  province: 'ON'
  url: 'https://www.uwo.ca/bmi/about/wirb.html'
  maps_id: ChIJCVSloavvLogR82_w3v729s0
organizers:
  - Ali Tafakkor
  - Peter Van Dyken
  - Rafaela Platkin
  - Anthony Cruz
  - Matthew Suppa Modrusan
  - Ricardo Alonso Rios Carrillo
  - Ronak Mohammady
  - Joud Abdulmajeed El-Shawa
  - Tallulah Grace Nyland
  - Ali Ghavampour
  - Kiro Samaan
  - Hanna Maekebay
  - Armin Panjehpour
  - Ali Khan
sponsors:
  - img: '/img/brainscan_logo.png'
    name: Brainscan
    url: 'https://brainscan.uwo.ca'
# Can support multiple, named schedules. Each schedule is a separate list item under
# schedule:
# For color, you can use "red", "green", and "blue", or any hex color or javascript
# colorname
schedule:
  - name: Tutorials
    startTime: 9
    endTime: 18
    days:
      - day: 26
        month: 3
        year: 2025
        events:
          - name: Welcome & Project Pitches
            time: '9:00'
            duration: '1:00'
            color: blue
            room:
              - WIRB 4190 (Lunchroom)
          - tutorial: prereg
            time: '10:00'
            duration: '1:00'
            color: '#007c62'
            room:
              - WIRB 4190 (Lunchroom)
            priority: 1
          # - tutorial: bayesian
          #   time: '10:00'
          #   duration: '1:00'
          #   color: green
          #   room:
          #     - TBD
          #   priority: 1
          - tutorial: eeg-bids
            time: '11:00'
            duration: '1:00'
            color: green
            room:
              - WIRB 4190 (Lunchroom)
          - name: Lunch
            time: '12:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
          - tutorial: hippunfold
            time: '13:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 1
            room:
              - WIRB 4190 (Lunchroom)
          - tutorial: 3dprint
            time: '14:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 1
            room: 
              - WIRB 4190 (Lunchroom)
          - tutorial: tms
            time: '15:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 1
            room: WIRB 4190 (Lunchroom)
      - day: 27
        month: 3
        year: 2025
        events:
          - name: Breakfast
            time: '9:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
          - name: Hack Time
            time: '10:00'
            duration: '2:00'
            room: WIRB 4190 (Lunchroom)
            color: '#222233'
            priority: 1
          - tutorial: writing
            time: '10:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 3000
          - tutorial: fnirs
            time: '11:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 3000
          - name: Lunch
            time: '12:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
          - name: Hack Time
            time: '14:00'
            duration: '2:00'
            room: WIRB 4190 (Lunchroom)
            color: '#222233'
            priority: 1
          - tutorial: mystmd
            time: '13:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 4190 (Lunchroom)
          - tutorial: reprod
            time: '14:00'
            duration: '1:00'
            color: '#007c62'
            priority: 2
            room: WIRB 3000
          - tutorial: monai
            time: '15:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 3000

      - day: 28
        month: 3
        year: 2025
        events:
          - name: Breakfast
            time: '9:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
          - name: Hack Time
            time: '10:00'
            duration: '2:00'
            room: WIRB 4190 (Lunchroom)
            color: '#222233'
            priority: 1
          - tutorial: git
            time: '10:00'
            duration: '1:00'
            color: '#007c62'
            priority: 2
            room: WIRB 3000
          - tutorial: datacol
            time: '11:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 3000
          - name: Lunch
            time: '12:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
          - name: Hack Time
            time: '13:00'
            duration: '1:00'
            room: WIRB 4190 (Lunchroom)
            color: '#222233'
            priority: 1
          # - tutorial: dataman
          #   time: '13:00'
          #   duration: '1:00'
          #   color: '#007c62'
          #   priority: 2
          #   room: WIRB 3000
          - tutorial: dti-mri
            time: '14:00'
            duration: '1:00'
            color: '#1f331e'
            priority: 2
            room: WIRB 4190 (Lunchroom)
          - tutorial: anat
            time: '13:00'
            duration: '2:00'
            color: '#1f331e'
            priority: 3
            room: WIRB 3000
          - name: Project presentations
            time: '15:00'
            duration: '1:00'
            color: blue
            room: WIRB 3000
          - name: Grad Club Networking Event
            time: '16:00'
            duration: '1:30'
            color: blue
            room: Grad Club
tutorials:
  - id: dti-mri
    name: Introduction to DTI and MRI
    organizer:
      - Bradley Karat
    image: /img/dfmri.png
    description: |
      This joint tutorial will cover both the basics of diffusion
      MRI and functional MRI. For diffusion MRI, the basics of processing data
      from MRI acquisitions to computing diffusion tensors and tracking the
      structural connectome will be covered. For functional MRI, the basics of
      what aspect of brain function fMRI measures to considerations for
      preprocessing fMRI data will be presented.
  - id: eeg-bids
    name: Using EEG-BIDS for data management of large EEG datasets
    organizer: Marc Joanisse
    image: /img/eegbids.png
    description: | 
      EEG-BIDS is a relatively new standard for the orderly storage of raw EEG/iEEG/MEG datasets and derivatives.
      I will demonstrate one possible workflow in which I use the EEGLAB toolbox to convert raw EEG data into BIDS format,
      and for integrating existing EEG-BIDS datasets into your analysis workflow.
  - id: fnirs
    name: Introduction to fNIRS
    organizer: 
      - Matthew Kolisnyk
      - Garima Gupta
    image: /img/fnirs2.png
    description: |
      Participants will learn the basics of functional near-infrared spectroscopy (fNIRS). This includes a demo of the system, the underlying physics and experimental design, as well as some exciting current applications of fNIRS. Participants will also learn about handling and preprocessing fNIRS data -- including some hands on coding!
  - id: anat
    name: 'Introduction to Neuroanatomy for Researchers'
    organizer:
      - Alaa Taha
      - Violet Liu
    image: '/img/afids.png'
    description: |
      This tutorial offers an interactive dive into neuroanatomy through a clinical case,
      with a focus on subcortical regions of interest.
      Participants will gain hands-on experience with segmentation tools like ITK-SNAP and learn to
      visualize subcortical structures using ultra-high field MRI.
      No previous experience with ITK-SNAP is required
      (http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.SNAP4)
  - id: tms
    name: 'Introduction to TMS'
    organizer: 
      - Phivos Phylactou
    image: '/img/tms2.png'
    description: Transcranial Magnetic Stimulation is a safe, non-invasive, tool that enables us to modulate the brain’s regular activity with high spatial and temporal resolution. Forty years since its introduction, TMS has been utilized in a variety of ways; from the labs all the way to the clinics. In this workshop, we will explore how TMS can be employed to causally study the brain’s neural architecture, how it can be used to measure brain activity, and how it can help the maladaptive brain.
  - id: prereg
    name: 'Open Science: Pre-registration'
    image: /img/prereg.png
    organizer:
      - Christine Moreau 
    description: In this hands-on workshop, participants will learn the fundamentals of preregistration and how it enhances research transparency and rigor using the Open Science Framework (OSF). Attendees are encouraged to bring their research protocols as there will be the opportunity to receive peer feedback to refine their preregistrations. The session will also cover handling protocol changes post-publication, emphasizing the flexibility of preregistration.
  - id: git
    name: 'Open Science: Research Code Management (Git)'
    image: /img/git-logo.png
    organizer:
      - Ali Tafakkor
      - Christine Moreau
    description: |
      This tutorial will cover best practices for managing research code with
      the ultimate goal of sharing it. Aspects of Git and GitHub, including
      version control, branching, collaborations, etc. will be covered.
  # - id: dataman
  #   name: 'Open Science: Research Data Management (DataLad)'
  #   image: /img/datalad.png
  #   organizer: Ali Tafakkor
  #   description: |
  #     Handling data can be a challenge, and it's best to think about it before
  #     you need to organize it on a deadline. In this tutorial you'll learn best
  #     practices for collecting, storing, processing, and sharing your data.
  #     We'll go over writing a Data Management Plan, formatting your data with
  #     BIDS and other open standards, and version controlling your data with
  #     DataLad, and uploading to a public repository.
  - id: reprod
    name: 'Open Science: Reproducible Data Analysis (Snakemake)'
    image: /img/snakemake_reproducable.png
    organizer: Ali Khan
    description: |
      Using a workflow management tool to run your research analyses can make it
      much easier to remember what you've done with your data, make small
      adjustments, and describe your analyses to others in a reproducible way.
      In this tutorial, you'll learn about what a workflow management tool is,
      why you might want to use one, and how to write your analyses as
      workflows. As an example, we'll go over SnakeBIDS, a Western-grown
      workflow management tool for handling BIDS-formatted neuroimaging data.
  # - id: mri
  #   name: A Brief Introduction to MRI
  #   image: /img/t1w.jpg
  #   organizer: Brad Karat
  #   description: |
  #     This tutorial will provide a basic introduction to MRI. We will cover
  #     where the MRI signal is originating from, what are the different
  #     contrasts, basic pulse sequences for acquiring an image, how to
  #     reconstruct and visualize an image from DICOM to NIFTI, and unique MRI
  #     contrasts such as diffusion or functional imaging.
  - id: writing
    name: Scientific Writing
    organizer:
      - Jessica Grahn
    image: /img/writing.png
    description: | 
      Want your scientific papers to be not just clear but also engaging? 
      Join our scientific writing style crash course at the hackathon! 
      Learn how to refine your tone, improve flow, and make your writing more compelling — without losing precision.
  - id: hippunfold
    name: HippUnfold Tutorial
    image: /img/hippunfold.png
    organizer: 
    - Ali Khan
    - Jordan DeKraker
    - Dhananjhay Bansal
    - Mackenzie Snyder
    description: |
      HippUnfold is a toolbox for automatically modeling the topological folding structure of the human hippocampus.
      This session will introduce its key features, including running HippUnfold, exploring volumetric and surface-based outputs,
      and integrating results with tools like ITK-SNAP and Connectome Workbench.
      We will also discuss applications to structural, fMRI, and dMRI data. No prior experience with HippUnfold is required.
      Links: https://github.com/khanlab/hippunfold
  - id: monai
    name: MONAI Tutorial
    organizer:
      - Mahmoud Salman
    image: /img/monai.png
    description: |
      A practical, no-theory guide to training deep learning models on neuroimaging data with zero experience. This tutorial covers MONAI, the leading AI framework for medical imaging, simplifying tasks like segmentation and classification. With pre-trained models, automated pipelines, and MONAI Zoo, you’ll apply deep learning to neuroscience research effortlessly—Python experience is required.
  - id: 3dprint
    name: 3D Printing Tutorial
    organizer:
      - Mehrdad Kashefi
      - Bassel Arafat
    image: /img/3dprint2.png
    description: | 
      Many experiments require rapid prototyping of experimental setups. While the traditional method of taping random parts together might work in a pinch, 3D printing offers a faster, more precise, and more robust solution. In this workshop, we’ll provide a brief overview of different 3D printing technologies and materials, followed by a hands-on tutorial on free, online 3D design software. As a fun bonus, we’ll show you how to turn your own MRI structural data into a 3D-printable model.
  - id: mystmd
    name: MystMD Tutorial
    organizer:
      - Ricardo Alonso Rios Carrillo
    image: /img/mystmd.png
    description: |
      This tutorial will introduce MystMD (https://mystmd.org/). MyST extends Markdown for technical, scientific communication and publication. MyST is an ecosystem of open-source, community-driven tools designed to revolutionize scientific communication.  
      The tutorial will cover installation and live code-writing of a short scientific article as a starting example. 
  - id: datacol
    name: 'Data Collection: Best Practices'
    organizer:
      - Sarah Hollywood
    image: /img/datacol.png
    description: This workshop centers around the best practices in the approach and conduct of data collection. This will include ethical considerations, how to effectively recruit participants and reduce attrition, improve your communication skills, and how these practices can make you a better researcher.

projects:
  2021:
    - title: BIDS - Creating the events.tsv file
      organizers:
        - name: Suzanne Witt
          github: switt4
      description: |
        While most of the steps to create a valid BIDS (Brain Imaging Data
        Structure) directory can be automated, the events.tsv file containing
        all of the experimental task information still needs to be largely dealt
        with manually. Making this process a bit more difficult is that for
        tasks that cannot be easily parameterized using just reaction time and
        correct responses, the current documentation is limited. For this
        project, I would like to gather anyone who is at the point of needing to
        make an events.tsv file for their own study and work on creating more
        user-friendly documentation for completing the events.tsv file with more
        real-world examples. And, if we decide it is needed, we will develop the
        framework for an app that will help researchers take their existing
        experimental output files and create a valid events.tsv file.
    - title: Automated skull-stripping fetal MRI data
      organizers:
        - name: Emily Nichols
      description: |
        My project has to do with skull-stripping fetal fMRI data - traditional
        tools don't work on fetal fMRI because of the surrounding tissue and the
        lack of a clear skull, which means 1000s of hours are spent manually
        segmenting the brain. There are some tools available, but they don't
        work well and still result in many hours spent fixing the automatic
        segmentations. I'm hoping to improve upon available tools so that
        automated segmentation works.
    - title: |
        Building a Jupyter Book tutorial for intracellular electrophysiology
        analysis in python
      organizers:
        - name: Sam Mestern
          github: sammestern
      description: |
        Intracellular electrophysiology experiments - specifically patch-clamp
        and its associated methodology - produce immense datasets consisting of
        highly structured time-series data. While many sub-fields of
        neuroscience have adopted standardized beginner-friendly computational
        analyses/tools, the intracellular patch-clamp field still lacks
        standardized & beginner-friendly analyses. Many intracellular papers
        rely on manual analysis with proprietary tools/code. For this brainhack
        project, we will build a [jupyter
        book](https://jupyterbook.org/intro.html) outlining some basic analysis
        that can be done on patch-clamp data, with a focus on building pipelines
        for batch analysis of patch-clamp data. The tutorials will utilize
        open-source tools from various sources, including the Allen institute!
        An early form of the notebooks can be found
        [here](https://www.smestern.com/PCCA_demo/intro.html).
    - title: Quality Control Visualization App
      organizers:
        - name: Peter Van Dyken
          github: pvandyken
      description: |
        Many automated pipelines include some sort of HTML based Quality Control
        output, allowing you to quickly scan through visualizations of the
        results. These are all in-house, custom solutions; there's no easy way
        to generate nice QC interfaces without manually creating html files. The
        goal of this project is to design a ReactJS based webapp that reads a
        JSON file containing a structured account of all the data to be
        displayed. For instance, the json would have paths to all the images to
        be displayed, organized by view, subject, contrast, task, or any other
        arbitrary dimension. The web app would automatically organize all of the
        data into a clean, modern web app interface, allowing the user to view
        the data along any dimension. In other words, you could easily view all
        the different contrasts from a single subject, with a given view, or
        view all the subjects across a given condition, or any other arbitray
        "slice" of the data.

        An app of this nature will be fairly complicated, so the goal during
        Brainhack would be to build a very basic prototype. Knowledge of
        Typescript (a typed superset of Javascript) and ReactJS will be helpful,
        but anyone interested in learning web app development is welcome.
        Knowledge or interest in graphic design (especially user interfaces)
        would also be useful.
  2022:
    - title: Safer Multimodal Teleoperation of (Simulated) Robots
      organizers:
        - name: Pranshu Malik
          github: 'pranshumalik14'
      description: |
        Being confused, freezing, or panicking while trying hard to stop,
        re-direct, or stabilize a drone (or any such robot/toy) in sudden
        counter-intuitive poses or environmental conditions is likely a
        relatable experience for all of us. The idea here is about enhancing the
        expression of our intent while controlling a robot remotely — either in
        real life or on a computer screen (simulation) — while not replacing the
        primary instrument of control (modality) but instead by also integrating
        our brain states (thought) in the control loop as measured, for example,
        through EEG. Specifically, for the scope of the hackathon, this could
        mean developing a brain-machine interface for automatically assisting
        the operator in emergency cases with “smart” control command reflexes or
        “takeovers”. Such an approach can be beneficial in high-risk cases such
        as remote handling of materials in nuclear facilities or it can also aid
        the supervision of autonomous control, say in the context of
        self-driving cars, to ultimately increase safety.

        For now, we could pick a particular type of simulated robot (industrial
        arms, RC cars, drones, etc.) and focus on designing and implementing a
        paradigm for characterizing intended motion and surprise during
        undesired motion in both autonomous (with no user control but robot's
        self- and environmental influences) or semi-autonomous cases (including
        user's control commands), i.e., we can aim to measure intent and
        surprise given the user's control commands, the brain states, and robot
        states during algorithmically curated cases of robot motion. This will
        help us detect such situations and also infer desired reactions to
        accordingly adjust control commands to achieve desired reactions during
        emergencies and, more generally, to augment real-time active control to
        match the desired motion. We can strive to keep the approach suitable
        for generalizing well enough to robots of other types and/or
        morphologies and to more unusual environments.
    - title: 'Brain3DVis: AR/MR MRI Visualizer'
      organizers:
        - name: Liam Bilbie
          github: LiamBilbie
      description: |
        Application that uses a web-based front end where users can submit brain
        MRI volumes. The data is then processed on the application backend, a 3D
        model is generated, and is then accessible in a AR/VR environment. We
        are using the MERN stack for the web component and C#/Unity for the
        AR/VR application. We would love to work with people who have experience
        with MRI volumetric segmentation or are interested in VR/AR data
        visualization. :slightly_smiling_face:
    - title: 'Functional Atlas Explorer'
      organizers:
        - name: Caroline Nettekoven
          github: carobellum
        - name: Ladan Shahshahani
          github: lshahsha
      description: |
        "What does the inferior frontal gyrus do?" Googling this question
        returns 93,400,000 results. A skim read of paper abstracts will give you
        some ideas about its functions. But wouldn't it be useful to have an
        interactive map where you can explore these functions in the brain?
        Imagine clicking on a brain region and getting a word cloud of functions
        that this region is highly involved in. That's what we will build!

        We will create an interactive tool, useful for anyone wanting to explore
        their own functional data or openly available functional datasets.
        Together with our functional fusion toolbox (in-house & soon to be
        released), it lets you integrate information from many different openly
        available datasets (Human Connectome Project, etc).

        During the project you will be able to use our existing toolbox to
        explore these large datasets - as well as your own data! In addition,
        this interactive map will provide a side by side view of your desired
        brain regions and their connections with other brain regions. Click on a
        region and you get a map of its functional connectivity to all other
        regions in the brain.

        The tool will help synthesize findings across studies (think Neurosynth,
        but directly based on fMRI data) and aid interpretation of results as
        well as planning of future experiments.
    - title: 'DWI Fiducials'
      organizers:
        - name: Arun Thurairajah
      description: |
        Diffusion-Weighted Imaging (DWI) is a variant of the standard MRI
        sequence examining the diffusion rate of water molecules.  DWI or
        Diffusion MRI has allowed for the improved study of white matter
        pathways across both diseased and healthy patients.

        The goal of the diffusion Fiducials or dFIDs project is to identify a
        set of anatomical landmarks on a variety of Diffusion-Weighted MRI
        images that are both salient and have functional significance.  This
        will be an extension of the previous Anatomical Fiducials (AFIDs)
        project that has localized a set of 32 clinically-relevant landmarks in
        humans, macaques, and PD patients in multiple imaging acquisitions (see
        https://doi.org/10.1002/hbm.24693).

        We are looking for students, researchers, and clinicians to determine
        potential fiducials across various acquisition types and models in DWI.
        Those with experience in acquiring diffusion images or who have an
        interest in neuroimaging or anatomy are welcome to join!
  2023:
    - title: DiffSimViz
      description: |
        DiffSimViz (Diffusion Simulator Visualizer) will be a python toolbox
        with the aim of providing intuitive visualizations of particle diffusion
        in different media/microstructure. This will ideally include an interface
        to choose particular media to visualize diffusion within as well as to
        change parameters such as diffusion time and membrane permeability. The
        use of such a visualizer will be didactic or for researchers to better
        understand what their diffusion MRI signal might look like in particular
        microstructural environments.
      url: https://github.com/Bradley-Karat/DiffSimViz
      organizers:
        - name: Bradley Karat
          github: Bradley-Karat
    - title: FunctionalSight
      description: |
        What happens in the brain stem when we move our eyes? And how can fMRI
        show us regions that control eye movements in different directions?
        FunctionalSight will allow researchers to (1) use eye tracking data to
        get components of eye movements and (2) regress these eye movement
        components into high-resolution fMRI data to understand how the brain
        stem controls the eyes. We will dive into high-resolution fMRI data
        acquired at Western and combine it with in-scanner eye tracking data to
        build a model that can show us the neural signatures of eye movements.
        Researchers will be able to use the model for their own eye tracking and
        fMRI data to better understand the neural basis of visual perception
        attention or reading. A guaranteed eye opening experience!
      organizers:
        - name: David Mekhaiel
          github: DavidMekhaiel
    - title: 'BrainLex: Engaging Neuroscience Glossary'
      description: |
        Navigating through neuroscience can be challenging as there are lots of
        complex terms to reference. BrainLex aims to solve this problem with an
        interactive online glossary suitable for all learners. Users can look up
        neuroscience terms and receive simple definitions visuals and links to related
        resources.
      organizers:
        - name: Parsa Abadi
          github: parsaabadi
    - title: Ciftipy
      description: |
        CiftiPy is a Python library designed to streamline the handling of complex CIFTI files used in neuroimaging research. CIFTI files represent gray matter as cortical surface vertices and subcortical volumes which often are difficult and time consuming to access and manipulate. CiftiPy simplifies this process providing an intuitive numpy-like interface for loading manipulating or creating CIFTI files. Built on top of the established Nibabel library, CiftiPy offers researchers a powerful yet user-friendly solution for working with CIFTI files enhancing the accessibility of advanced neuroimaging tools and workflows.
      url: https://github.com/pvandyken/ciftipy
      organizers:
        - name: Mohamed Yousif
          github: myousif9
  2025:
    - title: HippUnfold_v2.0
      description: |
        HippUnfold is a world-leading software for analysis of the hippocampus. The hippocampus is a "canary in a coal mine" brain region - a sensitive and early indicator of neurological conditions like dementia, epilepsy, and many others. It is also critical in memory and high-order cognition across all mammals. Some studies are already revealing HippUnfold's potential for translation to the clinic!

        Recently, we are creating a major overhaul of HippUnfold to run more lightly, smoothly, and using best-practices including BIDS, snakemake, and git continuous integration (version 2.0). We'd love to get input and/or help with outstanding issues on the new release, and would be especially keen to get feedback on its ease-of-use for new users and its Documentation.
        
        Come to the HippUnfold Tutorial at 1PM Wednesday for an introduction!

      url: https://github.com/khanlab/hippunfold
      organizers:
        - name: Jordan DeKraker
          github: jordandekraker
        - name: Ali Khan
          github: akhanf
    - title: Label Augmented Modality Agnostic Registration (LAMAR)
      description: |
        Registration can be tricky when there is low signal-to-noise ratio, signal dropout, and geometric distortions. This technique combines deep-learning based modality-agnostic segmentation with with conventional analytic registration methods to generate precise warpfields even in low-quality data. This type of registration can also be faster at higher resolutions, due to the simplicity of the label maps. The project will involve writing an optimizing python code, writing tests, some documentation, and assessing the quality of registration. This project is a good fit for anyone eager to learn more about python programming, registration, and convolutional neural networks, but even if you're brand new to everything, we can catch you up to speed!
      url: https://github.com/MICA-MNI/LaMAR
      organizers:
        - name: Ian Goodall-Halliwell
          github: Ian-Goodall-Halliwell
    - title: Diffusion Fiducials
      description: |
        Neurosurgical procedures, such as deep brain stimulation or lesion resection, depend on the precise alignment of multiple types of scans to accurately target specific structures. Currently, clinical quality control relies on visual inspection, which is insensitive to subtle yet significant misalignments. To address this, our lab developed the anatomical fiducials (AFIDs) framework comprising 32 easily identifiable anatomical landmarks to measure alignment accuracy at the millimetre scale. However, this protocol was only validated on T1-weighted (T1w) MRI scans showing anatomical information. In this project, we aim to extend and validate the AFIDs framework for diffusion MRI-derived functional anisotropy maps (FA maps), which show white matter tracks in the brain. We are looking for anyone interested in learning more about neuroanatomy to join our project apply the anatomical fiducial protocol to annotate FA maps!
      url: https://drive.google.com/drive/folders/1bfl6yQLSA4VBvbSgVSE7qjuQHfg8CVCy?usp=drive_link
      organizers:
        - name: Joy Zhao
          github: joy-zhao