TRAMPOLINO: the Swiss Army Knife for tractography

[matteomancini]

Guidelines

We are very excited to meet you at the 2020 OHBM Brainhack 🎉 To submit a project, you need to be an attendee of the 2020 OHBM Brainhack. We ask you to register first over here. Thank you!

We have prepared a checklist to help with your project submission. Here is how to proceed:

1. Before filling in any part, please submit this issue
2. Check items in the checklist below as you go through them
3. Once you are done (at least all 'required' items must be provided), please delete the "Guidelines" section add a comment saying 'hi @ohbm/project-monitors: My project is ready!'

Thank you!

After step 1 (issue submitted), we will assign a 'project monitor' to follow your submission. If at any time you need help or anything is unclear, please add a comment and ping your project monitor. Our team is here to help!

---

Project info

Title: TRAMPOLINO: the Swiss Army Knife for tractography

Project lead: Matteo Mancini @matteomancini

Timezone: London UTC+1

Hub: Europe, Middle East and Africa

Description:

I wrote TRAMPOLINO during BrainHack School with the idea of building a tool to easily do tractography across different packages. My vision now is to make it become the Swiss Army Knife for tractography: a tool able to try out things, even when you do not have the right software installed (!!!). The dream would be typing just "trampolino --corpus-callosum" and getting the tractogram for a corpus callosum to play with!

Link to project: https://github.com/matteomancini/trampolino

Mattermost handle: @matman

Goals for the OHBM Brainhack

• truly making TRAMPOLINO feels like a Swiss Army Knife!
• "just do it" arguments - to get immediately a tractogram to try stuff (e.g.: just typing "trampolino -track" would return a whole brain tractography for a sample subject);
• option to run workflows in containers;

Good first issues:

• write a script to easily retrieve public dataset;
• implement tractography format conversions (e.g. .tck->.trk);
• write Nipype workflows and/or interfaces for Diffusion Toolkit ODFs and Trekker;

Skills:

• Python;
• Interest in tractography;
• Nipype and Click packages (useful skill but not necessary);
• Some experience with any existing tractography package would be a plus;

Chat channel: hbmhack-trampolino

Video channel:
Please have a look at the Mattermost channel for the URL of the video channel, or alternatively, please contact to @matman on Mattermost.

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

• Link to your project: could be a code repository, a shared document, etc. See here
• Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
• Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• Video channel: Please create a video channel that will be used during the OHBM Brainhack and share it in your chat channel above. This can be an existing channel or a new one. For instance a jitsi meet room, cf. here.

You can also include information about (all optional):

• Number of participants, cf. here
• Twitter-size summary of your project pitch, cf. here
• Provide an image of your project for the OHBM brainhack website
• Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

• Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
• Provide links to onboarding documents if you have some.

[welcome]

(Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808)
🎉 Welcome to the 2020 OHBM Hackathon! 🎉 We're really excited to have your input on this repository and welcome your idea! 💖 If you haven't done so already, please make sure you check out our Code of Conduct. Did you issue a new hackathon project? Please check if you have provided all relevant information and an image for the website.

[llevitis]

Hi @matteomancini ! This project sounds like a great idea, and it makes me even happier that this is something that you started during BHS :) I've added a few more labels to the project based on the description you provided.

[matteomancini]

HI @llevitis thanks for the feedback! I just updated the Mattermost channel name following @Remi-Gau advice. I have a question: I noticed only after submitting that at least one of the skills should be a non-coding one. Would "experience with the command line" be considered as non-coding? If it is the case, I will add it, because someone willing to just test stuff and write documentation would be more than welcome.

[Naubody]

Hi @matteomancini, very cool project! I'm Matthias and I will make sure your work will be communicated on Twitter ;-)

[DorienHuijser]

Hi @matteomancini, is there an image that you would like to display with your project on the hackathon website? If so, let me know. Thanks!

[matteomancini]

Hi @DorienHuijser the one already used on Twitter should do the job: https://twitter.com/OhbmOpen/status/1271113044987445254
Thanks! (:

[complexbrains]

Dear @matteomancini Would you mind sharing the video link for your project in your Mattermost channel and pining it to the channel please? Also could you please let us know regarding completion of this then we will complete the revision for you. Thank you 🤗

[matteomancini]

Hi @complexbrains I just pinned the video link to the Mattermost channel.

[complexbrains]

Thank you @matteomancini Then your project seems ready to go! Welcome aboard! 🤗 🎊

[matteomancini]

This is my twitter-size summary of my pitch (in a thread of three tweets):

There are so many great software package to do tractography. My initial goal with TRAMPOLINO was to create a tool to compare packages through a common interface, to explore different algorithms and the influence of parameters. (1/3)

Right now, you can run a whole workflow or a subset of it for three popular tractography software, leveraging on Nipype and click. Is it enough? I still find myself having an idea or wanting to try something, but without a simple tool to quickly do it. (2/3)

My goal for OHBM BrainHack 2020 is building a Swiss Army Knife for tractography. Try a package without installing it? Need some data quickly? A corpus callosum on the fly? That would be a job for TRAMPOLINO! https://github.com/matteomancini/trampolino #OHBMhackathon #BrainHack #OHBM2020 (3/3)