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brainhackorg / global2020

Brainhack Global 2020
https://brainhack.org/global2020/
MIT License
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Task-based connectivity analysis for functional NIRS data #37

Open CesarCaballeroGaudes opened 3 years ago

CesarCaballeroGaudes commented 3 years ago

Project info

Title: Task-based connectivity analysis for functional NIRS data

image

Project lead:

Borja Blanco, twitter.com/borja_blanco4 Irene Arrieta, twitter.com/irenearrieta3

Project collaborators:

César Caballero-Gaudes, twitter.com/CaballeroGaudes Mattermost: @CesarCaballeroGaudes Eneko Uruñuela, twitter.com/eurunuela Mattermost: @eurunuela

Registered Brainhack Global 2020 Event:

Brainhack Donostia 2020, San Sebastián-Donostia

Project Description: The aim of this project is to learn, comprehend and implement implement two types of task-based connectivity analyses for functional near infrared spectroscopy (fNIRS) data, namely generalized psycho-physiological interactions (gPPI) and Dynamic Causal Modelling (DCM). These approaches will be evaluated in fNIRS data collected in 4-month-old infants while they listened to forward and backward speech sentences during sleep. Coding will mostly be in MATLAB (similar to the main programs for fNIRS data analysis), although implementation in Python can be explored.

Data to use:

Datasets to work with will be available in project's GitHub repo (see next).

Link to project repository/sources: https://github.com/borjablanco/BHDonostia_2020_fNIRS

Goals for Brainhack Global 2020:

The goals of the project will be split into two different parts and days. Days 1-3:

Days 4 and 5:

Good first issues:

Recommended Readings: gPPI:

  1. Gitelman, D.R., Penny, W.D., Ashburner, J. and Friston, K.J., 2003. Modeling regional and psychophysiologic interactions in fMRI: the importance of hemodynamic deconvolution. Neuroimage, 19(1), pp.200-207. https://doi.org/10.1016/S1053-8119(03)00058-2
  2. McLaren, D.G., Ries, M.L., Xu, G. and Johnson, S.C., 2012. A generalized form of context-dependent psychophysiological interactions (gPPI): a comparison to standard approaches. Neuroimage, 61(4), pp.1277-1286. https://doi.org/10.1016/j.neuroimage.2012.03.068
  3. Hassanpour, M.S., Eggebrecht, A.T., Peelle, J.E. and Culver, J.P., 2017. Mapping effective connectivity within cortical networks with diffuse optical tomography. Neurophotonics, 4(4), p.041402. https://doi.org/10.1117/1.NPh.4.4.041402
  4. Gerchen, M.F., Bernal‐Casas, D. and Kirsch, P., 2014. Analyzing task‐dependent brain network changes by whole‐brain psychophysiological interactions: A comparison to conventional analysis. Human brain mapping, 35(10), pp.5071-5082. https://doi.org/10.1002/hbm.22532

DCM:

  1. Tak, S., Kempny, A., Friston, K.J., Leff, A.P. and Penny, W.D., 2015. Dynamic causal modelling for functional near-infrared spectroscopy. Neuroimage, 111, pp.338-349. https://doi.org/10.1016/j.neuroimage.2015.02.035
  2. Bulgarelli, C., Blasi, A., Arridge, S., Powell, S., de Klerk, C.C., Southgate, V., Brigadoi, S., Penny, W., Tak, S. and Hamilton, A., 2018. Dynamic causal modelling on infant fNIRS data: A validation study on a simultaneously recorded fNIRS-fMRI dataset. NeuroImage, 175, pp.413-424. https://doi.org/10.1016/j.neuroimage.2018.04.022
  3. Chapter 46 of SPM12 Manual. https://www.fil.ion.ucl.ac.uk/spm/doc/spm12_manual.pdf

Skills:

Communication channels:

## Project Submission ### Submission checklist *Once the issue is submitted, please check items in this list as you add under ‘Additional project info’* - [ ] Link to your project: could be a code repository, a shared document, etc. - [ ] Goals for Brainhack Global 2020: describe what you want to achieve during this brainhack. - [ ] 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. - [ ] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill. Use the issue labels for this purpose.

Optionally, you can also include information about:

We would like to think about how you will credit and onboard new members to your project. If you’d like to share your thoughts with future project participants, you can include information about:

eurunuela commented 3 years ago

Thank you so much for submitting this project @CesarCaballeroGaudes !

I see you have two things missing on your checklist that are required for the project to be submitted:

  1. Link to your project: could be a code repository, a shared document, etc.
  2. Chat channel: A link to a chat channel that will be used during the Brainhack Global 2020 event. This can be an existing channel or a new one. We recommend using the Brainhack space on Mattermost.

I think we can publish the project to the website once these two points are done.

Thank you! 🙌🏻

CesarCaballeroGaudes commented 3 years ago

Here is the logo for the project image

eurunuela commented 3 years ago

Hey @SamGuay , this one's ready too. I thought the web_ready label triggered the action but maybe not?

Also, how do we make the logo appear on the website?

Thanks!

SamGuay commented 3 years ago

Also, how do we make the logo appear on the website?

Love the pic! If you want to add a picture, simply edit your issue and paste the picture somewhere in there, the regex will find it! If it were me, I'd add it somewhere at the top. Maybe I should add a note into the template for the picture.

I thought the web_ready label triggered the action but maybe not?

Eventually it will. Right now it is human action and not a GH action :sweat_smile:.

eurunuela commented 3 years ago

Thank you @CesarCaballeroGaudes

Logo is ready. Could you please publish it @SamGuay ?

complexbrains commented 3 years ago

Dear @CesarCaballeroGaudes I just wanted to ask whether would you like to continue your projects throughout the upcoming 3 weeks time of Brainhack Global events or would you be available to the contributions? We would be happy to see contributions from other locations to your project still going, but sure based on your availability and so on. So just wanted to raise your attention to the possible interactions might be happening and ask again your current position accordingly if we get any question regarding your project.

Thank you very much for your contribution and amazing project throughout Brainhack Donostia :hugs: 🚀

CesarCaballeroGaudes commented 3 years ago

Yes, we would welcome anyone in the project!!

complexbrains commented 3 years ago

Perfect! We will make the announcement accordingly. In the meantime, it might be better to register with one of those events their dates listed below that suits with your own schedule, and then run your project under those events It might just help with the advertising and getting attention from those event attendees too. Please let us know your decision on that then we will change the event label for you to make people from that event location especially to find you. Does that sound alright to you? Here are the events

|9 Dec - 11 th Dec, 2020 | Brainhack Pittsburgh| |1stDec - 3rd Dec, 2020 | Brainhack Ankara| |30th Nov - 11th Dec, 2020 |Brainhack Marburg| |2nd Dec - 4th Dec, 2020 |Brainhack Ontario| |2nd Dec - 4th Dec, 2020 |Brainhack Marseille| |6th Dec - 11th Dec, 2020 |Brainhack Princeton| |11th Dec -13th Dec, 2020 |Brainhack NY| |12th Dec -13th Dec, 2020 | Brainhack DC| |12th Dec - 18th Dec, 2020 | Brainhack Growth Chart Translation - Beijing - Nanning| |14th Dec to 16th Dec, 2020 |Brainhack Padova: Diversity Inter-individual variability in cognitive and clinical neuroscience: signal or noise?|

I will also make the announcements again at the main Mattermost channels to attract people to your projects. Thank you so much for your contribution indeed. It is really nice of you and hope you get nice interactions again :hugs: