From b485d2db3184bd365df8d81cd342abee08991e75 Mon Sep 17 00:00:00 2001 From: Remi-Gau Date: Thu, 7 Dec 2023 16:37:53 +0000 Subject: [PATCH] deploy: cbe91bb9cdd8041737889e605934d1e5305fac57 --- index.html | 2 +- index.json | 2 +- project/project_30/index.html | 4 +- project/project_31/index.html | 4 +- project/project_33/index.html | 4 +- project/project_44/index.html | 4 +- project/project_60/index.html | 4 +- project/project_61/index.html | 4 +- project/project_63/index.html | 4 +- project/project_67/index.html | 4 +- project/project_71/index.html | 4 +- project/project_74/index.html | 2 +- project/project_75/index.html | 2 +- projects/index.html | 314 +++++++++++++++++----------------- sitemap.xml | 2 +- 15 files changed, 180 insertions(+), 180 deletions(-) diff --git a/index.html b/index.html index 730d244..d733bc8 100644 --- a/index.html +++ b/index.html @@ -44,7 +44,7 @@ Brainhack Global 2023!

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The Brainhack Global team built up a set of resources for you to help you organize your local Brainhack including guidelines, checklists, template forms, press release materials and more.

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Meet the Team

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Kelly Garner

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Johanna Bayer

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Christopher Nolan

Outreach and DEI

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Stephanie Noble

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diff --git a/index.json b/index.json index 62e3d9c..489bd87 100644 --- a/index.json +++ b/index.json @@ -1 +1 @@ -[{"authors":["Cameron Craddock"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1679385743,"objectID":"b02f535844ad6f9708d52e0fbccc8341","permalink":"https://www.brainhack.org/global2023/author/cameron-craddock/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/global2023/author/cameron-craddock/","section":"authors","summary":"","tags":null,"title":"Cameron Craddock","type":"authors"},{"authors":["Christopher 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Pydra","type":"project"},{"authors":null,"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1701967056,"objectID":"f0d0d93b0a5c9812281adb97d3527f47","permalink":"https://www.brainhack.org/global2023/project/project_71/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/global2023/project/project_71/","section":"project","summary":"","tags":null,"title":"The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI","type":"project"}] \ No newline at end of file diff --git a/project/project_30/index.html b/project/project_30/index.html index 1270090..f82aef8 100644 --- a/project/project_30/index.html +++ b/project/project_30/index.html @@ -1,7 +1,7 @@ -Clustintime: a toolbox for spatio-temporal clustering of fMRI data | Brainhack Global 2023

Clustintime: a toolbox for spatio-temporal clustering of fMRI data

Last updated on -Nov 21, 2023

Title

Clustintime: a toolbox for spatio-temporal clustering of fMRI data

Leaders

Cris Tobías (@cristobias)

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

  • What are you doing, for whom, and why? +Dec 7, 2023

Title

Clustintime: a toolbox for spatio-temporal clustering of fMRI data

Leaders

Cris Tobías (@cristobias)

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

  • What are you doing, for whom, and why? This project is a toolbox that allows researchers in neuroimage to apply clustering methods to fMRI data on the spatiotemporal domain. Conventional methods of clustering in fMRI allow to see spatial patterns but cannot describe the temporal dynamics of functional activity.

  • What makes your project special and exciting? Providing a tool for researchers interested in analyzing brain patterns in uncontrolled fmri experiments or clinical settings is a necessity that has not been covered yet and that could be done through clustintime.

  • How to get started? Clustintime has been under development for a few years and has been already tried on data from individual epileptic patients, the skeletton of the project is already done, now there is need to transform it into a proper toolbox to release the first version of the software.

  • Where to find key resources? diff --git a/project/project_31/index.html b/project/project_31/index.html index 492e21a..834b65e 100644 --- a/project/project_31/index.html +++ b/project/project_31/index.html @@ -1,7 +1,7 @@ -Tedana: TE-dependent analysis | Brainhack Global 2023

    Tedana: TE-dependent analysis

    Last updated on -Nov 17, 2023

    Title

    Tedana: TE-dependent analysis

    Leaders

    Eneko Uruñuela (@eurunuela)

    Collaborators

    No response

    Brainhack Global 2023 Event

    Brainhack Donostia

    Project Description

    • What are you doing, for whom, and why?
    • What makes your project special and exciting?
    • How to get started?
    • Where to find key resources?

    https://github.com/ME-ICA/tedana

    Goals for Brainhack Global

    They are listed in the following GitHub discussion: https://github.com/ME-ICA/tedana/discussions/987

    Good first issues

    1. issue one: Fix reference rendering in HTML report

    2. issue two: Documentation to highlight situations or studies where multi-echo or tedana are specifically useful

    Communication channels

    https://mattermost.brainhack.org/brainhack/channels/tedana

    Skills

    • Python: beginner/medium
    • Documentation: beginner

    Onboarding documentation

    https://github.com/ME-ICA/tedana/blob/main/CONTRIBUTING.md

    What will participants learn?

    • How small scientific open-source software development happens
    • How to contribute to such projects
    • How tedana works for multi-echo fMRI denoising
    • How to use GitHub

    Data to use

    Multi-echo data we use to test tedana is available in OSF: https://osf.io/bpe8h/

    Number of collaborators

    2

    Credit to collaborators

    Project contributors are listed on the project README using the all contributors bot:

    https://github.com/ME-ICA/tedana

    Image

    Leave this text if you don’t have an image yet.

    Type

    documentation, method_development, visualization

    Development status

    2_releases_existing

    Topic

    ICA, PCA

    Tools

    other

    Programming language

    documentation, Python, html_css

    Modalities

    fMRI

    Git skills

    0_no_git_skills

    Anything else?

    No response

    Things to do after the project is submitted and ready to review.

    • Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
    • Twitter-sized summary of your project pitch.

    Date
    Jan 1, 0001 12:00 AM
    +Dec 7, 2023

Title

Tedana: TE-dependent analysis

Leaders

Eneko Uruñuela (@eurunuela)

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

  • What are you doing, for whom, and why?
  • What makes your project special and exciting?
  • How to get started?
  • Where to find key resources?

https://github.com/ME-ICA/tedana

Goals for Brainhack Global

They are listed in the following GitHub discussion: https://github.com/ME-ICA/tedana/discussions/987

Good first issues

  1. issue one: Fix reference rendering in HTML report

  2. issue two: Documentation to highlight situations or studies where multi-echo or tedana are specifically useful

Communication channels

https://mattermost.brainhack.org/brainhack/channels/tedana

Skills

  • Python: beginner/medium
  • Documentation: beginner

Onboarding documentation

https://github.com/ME-ICA/tedana/blob/main/CONTRIBUTING.md

What will participants learn?

  • How small scientific open-source software development happens
  • How to contribute to such projects
  • How tedana works for multi-echo fMRI denoising
  • How to use GitHub

Data to use

Multi-echo data we use to test tedana is available in OSF: https://osf.io/bpe8h/

Number of collaborators

2

Credit to collaborators

Project contributors are listed on the project README using the all contributors bot:

https://github.com/ME-ICA/tedana

Image

Leave this text if you don’t have an image yet.

Type

documentation, method_development, visualization

Development status

2_releases_existing

Topic

ICA, PCA

Tools

other

Programming language

documentation, Python, html_css

Modalities

fMRI

Git skills

0_no_git_skills

Anything else?

No response

Things to do after the project is submitted and ready to review.

  • Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
  • Twitter-sized summary of your project pitch.

Date
Jan 1, 0001 12:00 AM
diff --git a/project/project_33/index.html b/project/project_33/index.html index 15675e5..0d57dd6 100644 --- a/project/project_33/index.html +++ b/project/project_33/index.html @@ -1,7 +1,7 @@ -phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping | Brainhack Global 2023

phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

Last updated on -Nov 17, 2023

Title

phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

Leaders

Stefano Moia

Email: s.moia.research@gmail.com +Dec 7, 2023

Title

phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

Leaders

Stefano Moia

Email: s.moia.research@gmail.com Twitter: @SteMoia Mattermost: @smoia

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

phys2cvr is a python toolbox that aims at offering various approaches to compute cerebrovascular mapping, starting from at least a functional MRI hypervolume.

While not the first toolbox to compute CVR out there, I’m aiming at making something easy to adopt, a swiss knife to compute all sorts of maps to image cerebral physiology (not to denoise fMRI timeseries, for that you can check phys2denoise ). phys2cvr should become one of the most complete tools for CVR mapping available, easy to adopt through a CLI (and, if possible, a GUI), with nice reports and plots, and allowing the highest automation through BIDS compliance. No repetition allowed thoough: for all python-based approaches out there, phys2cvr should only act as wrap around. diff --git a/project/project_44/index.html b/project/project_44/index.html index 2e84c9f..6037a33 100644 --- a/project/project_44/index.html +++ b/project/project_44/index.html @@ -1,7 +1,7 @@ -Launchcontainers: A Python tool for launching containerized analysis on HPC | Brainhack Global 2023

Launchcontainers: A Python tool for launching containerized analysis on HPC

Last updated on -Nov 17, 2023

Title

Launchcontainers: A Python tool for launching containerized analysis on HPC

Leaders

Yongning Lei

email: t.lei@bcbl.eu

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

Launchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program takes one config.ymal file, one container.json file, and one subject-session-list.txt file as inputs. Using 1 line of bash command, it will automatically send jobs to HPC clusters regarding your computing demands.

This program is well-suited for multi-subject, multi-scan datasets. And it will save a lot of time if you need analysis your entire dataset with different parameters multiple times.

In future versions, we are trying to add more functionality to this repository so that you can launch all the MRI data analysis pipelines such as Heudiconv, fMRIprep, pRF pipelines and etc. Please keep track of this repo and if you have any questions or suggestions, don’t hesitate to contact Gari: garikoitz@gmail.com +Dec 7, 2023

Title

Launchcontainers: A Python tool for launching containerized analysis on HPC

Leaders

Yongning Lei

email: t.lei@bcbl.eu

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

Launchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program takes one config.ymal file, one container.json file, and one subject-session-list.txt file as inputs. Using 1 line of bash command, it will automatically send jobs to HPC clusters regarding your computing demands.

This program is well-suited for multi-subject, multi-scan datasets. And it will save a lot of time if you need analysis your entire dataset with different parameters multiple times.

In future versions, we are trying to add more functionality to this repository so that you can launch all the MRI data analysis pipelines such as Heudiconv, fMRIprep, pRF pipelines and etc. Please keep track of this repo and if you have any questions or suggestions, don’t hesitate to contact Gari: garikoitz@gmail.com and Tiger: t.lei@bcbl.eu

https://github.com/garikoitz/launchcontainers

Goals for Brainhack Global

  • Let more people get to know the advantages of using containers to process MRI data to improve the data availability and reproducibility
  • Let beginner level users get familiar with the UNIX operation and git operation
  • Add new features to launchcontainer so that it supports more MRI processing pipeline (ie. HeuDiconv, fMRIprep, PRF-analyze)
  • Make a better documentation on the project Wiki

Good first issues

  1. issue one: https://github.com/garikoitz/launchcontainers/issues/28
  2. issue two: https://github.com/garikoitz/launchcontainers/issues/32

Communication channels

https://mattermost.bcbl.eu/bhdonostia/channels/launchcontainer

Skills

  • Python intermediate
  • Unix intermediate

Onboarding documentation

https://docs.google.com/document/d/1XMmMpp3w7i2o8wVyHv_kUgoTgYVJ7n-qvgIQilfEBEU/edit?usp=sharing

What will participants learn?

  • How to use Unix to run python script, navigate to directory, and edit files.
  • How to use git to collaborate with other’s, create branch to fix issues, pull-request
  • How to use launchcontainers to launch DWI pipeline on SGE, SLURM and local machine

Data to use

I will prepare the converted nifti DWI scan folder in BIDS format and zipped it for use

Number of collaborators

3

Credit to collaborators

Project contributers will be listed in the launchcontainer repo

Image

Launchcontainer logo

Type

documentation coding_methods

Development status

2_releases_existing

Topic

reproducible_scientific_methods

Tools

BIDS

Programming language

Python

Modalities

DWI

Git skills

1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

  • Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
  • Twitter-sized summary of your project pitch.

Date
Jan 1, 0001 12:00 AM
diff --git a/project/project_60/index.html b/project/project_60/index.html index 19086f2..14734fc 100644 --- a/project/project_60/index.html +++ b/project/project_60/index.html @@ -1,7 +1,7 @@ -Psy2R: Developing an R package for better inference in multivariate statistical analysis | Brainhack Global 2023

Psy2R: Developing an R package for better inference in multivariate statistical analysis

Last updated on -Nov 21, 2023

Title

Psy2R: Developing an R package for better inference in multivariate statistical analysis

Leaders

Kelly Garner Github: @kel-github Mattermost: @kels

Collaborators

Kevin Bird,
Melanie Gleitzman,
Sonny Li,
Christopher Nolan Github: @crnolan Mattermost: @cnolan

Brainhack Global 2023 Event

Brainhack Australasia

Project Description

We consistently use massive data sets across neuroscience and psychology. The routine gathering of big data requires that we are well equipped with tools that allow us to conduct appropriate multivariate statistics.

Multivariate statistical analysis typically follows a two stage procedure, an omnibus test of the global null hypothesis followed by post-hoc tests of specific effects. It is not well known that under certain circumstances this leads to a drastically inflated rate of type 1 error. It is even less well known that this procedure can also lead to an even lessor known type IV error (incorrect interpretation of a correctly rejected hypothesis)!

It is possible to avoid these dragons by using an alternative procedure where all inferences are derived from simultaneous confidence intervals (SCIs) on contrasts of interest. This approach provides interval inferences on effect sizes and it also ensures that the familywise type 1 error rate associated with directional inferences (the inferences usually derived from tests of null hypotheses) is controlled at alpha. One piece of software (PSY) can produce SCIs appropriate for planned analyses (where contrasts are defined independently of the data) and for more flexible analyses where contrasts are defined on a post hoc basis. However, this software is only available for use on windows and cannot be scripted into reproducible workflows.

Our goal is to build an R package that implements the functions of PSY, and to make this method of statistical inference available to the masses!

TBC

Goals for Brainhack Global

Milestones

  1. Implement analyses that can be done in PSY in R [intermediate]
  2. Convert R implementation into generalisable functions [intermediate/advanced]
  3. Outline the math involved in computing critical values for STP tests under the null hypothesis [advanced]
  4. Interpret the PASCAL code that underpins the computation of critical values in PSY [advanced]
  5. Investigate the R world for a comprehensive list of packages that share some functionality with PSY [beginner]
  6. Test R functions and implement own analysis [beginner]
  7. Interpret what you think our R code does, to help us write more readable code [beginner]
  8. Document the PSY software functions and write documentation for the new R functions [beginner]
  9. Create project management board (e.g. trello) to keep us on track! [beginner]

Good first issues

  1. Implement analyses that can be done in PSY in R

  2. Document existing PSY software functions

  3. Investigate the R world for a comprehensive list of packages that share some functionality with PSY

  4. Create project management board (e.g. trello) to keep us on track!

  5. Create github repo for the project

Communication channels

https://mattermost.brainhack.org/brainhack/channels/psy2r

Skills

  • R: all levels
  • stats/math: all levels
  • github: all levels
  • comp sci: intermediate/advanced

Onboarding documentation

No response

What will participants learn?

You’ll learn more about statistical analysis of big datasets, collaborative coding using R and github, and hopefully a bit about package development and coding for other users.

Data to use

No response

Number of collaborators

more

Credit to collaborators

Project contributors will be listed on the github repository’s README.md

Image

DALL·E 2023-11-19 14 53 27 - draw me the greek character ‘psi’ with a capital R beside it in Quentin Blake style watercolour

Type

coding_methods, data_management, documentation, method_development

Development status

0_concept_no_content

Topic

reproducible_scientific_methods, statistical_modelling

Tools

other

Programming language

C++, documentation, R, other

Modalities

behavioral, DWI, ECOG, EEG, eye_tracking, fMRI, MEG, MRI, PET

Git skills

1_commit_push

Anything else?

No response

Things to do after the project is submitted and ready to review.

  • Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
  • Twitter-sized summary of your project pitch.

Date
Jan 1, 0001 12:00 AM
+Dec 7, 2023

Title

Psy2R: Developing an R package for better inference in multivariate statistical analysis

Leaders

Kelly Garner Github: @kel-github Mattermost: @kels

Collaborators

Kevin Bird,
Melanie Gleitzman,
Sonny Li,
Christopher Nolan Github: @crnolan Mattermost: @cnolan

Brainhack Global 2023 Event

Brainhack Australasia

Project Description

We consistently use massive data sets across neuroscience and psychology. The routine gathering of big data requires that we are well equipped with tools that allow us to conduct appropriate multivariate statistics.

Multivariate statistical analysis typically follows a two stage procedure, an omnibus test of the global null hypothesis followed by post-hoc tests of specific effects. It is not well known that under certain circumstances this leads to a drastically inflated rate of type 1 error. It is even less well known that this procedure can also lead to an even lessor known type IV error (incorrect interpretation of a correctly rejected hypothesis)!

It is possible to avoid these dragons by using an alternative procedure where all inferences are derived from simultaneous confidence intervals (SCIs) on contrasts of interest. This approach provides interval inferences on effect sizes and it also ensures that the familywise type 1 error rate associated with directional inferences (the inferences usually derived from tests of null hypotheses) is controlled at alpha. One piece of software (PSY) can produce SCIs appropriate for planned analyses (where contrasts are defined independently of the data) and for more flexible analyses where contrasts are defined on a post hoc basis. However, this software is only available for use on windows and cannot be scripted into reproducible workflows.

Our goal is to build an R package that implements the functions of PSY, and to make this method of statistical inference available to the masses!

TBC

Goals for Brainhack Global

Milestones

  1. Implement analyses that can be done in PSY in R [intermediate]
  2. Convert R implementation into generalisable functions [intermediate/advanced]
  3. Outline the math involved in computing critical values for STP tests under the null hypothesis [advanced]
  4. Interpret the PASCAL code that underpins the computation of critical values in PSY [advanced]
  5. Investigate the R world for a comprehensive list of packages that share some functionality with PSY [beginner]
  6. Test R functions and implement own analysis [beginner]
  7. Interpret what you think our R code does, to help us write more readable code [beginner]
  8. Document the PSY software functions and write documentation for the new R functions [beginner]
  9. Create project management board (e.g. trello) to keep us on track! [beginner]

Good first issues

  1. Implement analyses that can be done in PSY in R

  2. Document existing PSY software functions

  3. Investigate the R world for a comprehensive list of packages that share some functionality with PSY

  4. Create project management board (e.g. trello) to keep us on track!

  5. Create github repo for the project

Communication channels

https://mattermost.brainhack.org/brainhack/channels/psy2r

Skills

  • R: all levels
  • stats/math: all levels
  • github: all levels
  • comp sci: intermediate/advanced

Onboarding documentation

No response

What will participants learn?

You’ll learn more about statistical analysis of big datasets, collaborative coding using R and github, and hopefully a bit about package development and coding for other users.

Data to use

No response

Number of collaborators

more

Credit to collaborators

Project contributors will be listed on the github repository’s README.md

Image

DALL·E 2023-11-19 14 53 27 - draw me the greek character ‘psi’ with a capital R beside it in Quentin Blake style watercolour

Type

coding_methods, data_management, documentation, method_development

Development status

0_concept_no_content

Topic

reproducible_scientific_methods, statistical_modelling

Tools

other

Programming language

C++, documentation, R, other

Modalities

behavioral, DWI, ECOG, EEG, eye_tracking, fMRI, MEG, MRI, PET

Git skills

1_commit_push

Anything else?

No response

Things to do after the project is submitted and ready to review.

  • Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
  • Twitter-sized summary of your project pitch.

Date
Jan 1, 0001 12:00 AM
diff --git a/project/project_61/index.html b/project/project_61/index.html index caf9611..1385862 100644 --- a/project/project_61/index.html +++ b/project/project_61/index.html @@ -1,7 +1,7 @@ -The evolution of Nipype into Pydra | Brainhack Global 2023

The evolution of Nipype into Pydra

Last updated on -Nov 21, 2023

Title

The evolution of Nipype into Pydra

Leaders

Tom Close (GH+MM: @tclose) and Arkiev D’Souza (GH: @arkiev MM: adsouza)

Collaborators

Dorota Jarecka (GH: @djarecka MM: dorota), Chris Markiewicz (GH: @effigies, MM: markiewicz), Yibei Chen (GH: @yibeichan MM: yibeichen), Ghislain Vaillant (GH+MM: @ghisvail) and Satra Ghosh (GH+MM: @satra)

Brainhack Global 2023 Event

Brainhack Australasia

Project Description

Nipype +Dec 7, 2023

Title

The evolution of Nipype into Pydra

Leaders

Tom Close (GH+MM: @tclose) and Arkiev D’Souza (GH: @arkiev MM: adsouza)

Collaborators

Dorota Jarecka (GH: @djarecka MM: dorota), Chris Markiewicz (GH: @effigies, MM: markiewicz), Yibei Chen (GH: @yibeichan MM: yibeichen), Ghislain Vaillant (GH+MM: @ghisvail) and Satra Ghosh (GH+MM: @satra)

Brainhack Global 2023 Event

Brainhack Australasia

Project Description

Nipype is a Python library that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. It forms the basis of widely-used pipelines such as C-PAC and fMRIPrep .

Despite Nipype’s success and longevity, some limitations of its design have become apparent over time. In particular,

  • the complexity of designing new task interfaces
  • inability to run workflow nodes in separate software containers
  • inability to split/join workflow nodes over lists generated at execution time
  • difficulty following the workflow construction syntax due to the separation of nodes and connections

Therefore, at the 2018 OHBM BrainHack in Singapore, a number of Nipype’s core developers sat down to start planning a rewritten 2nd generation, which eventually turned into Pydra diff --git a/project/project_63/index.html b/project/project_63/index.html index 1841753..9607ac5 100644 --- a/project/project_63/index.html +++ b/project/project_63/index.html @@ -1,7 +1,7 @@ -behapy: A behavioural neuroscience analysis package for Python | Brainhack Global 2023

behapy: A behavioural neuroscience analysis package for Python

Last updated on -Nov 20, 2023

Title

behapy: A behavioural neuroscience analysis package for Python

Leaders

Chris Nolan (Mattermost: @cnolan | Mastodon: @cnolan@fediscience.org)

Collaborators

Thomas Burton +Dec 7, 2023

Title

behapy: A behavioural neuroscience analysis package for Python

Leaders

Chris Nolan (Mattermost: @cnolan | Mastodon: @cnolan@fediscience.org)

Collaborators

Thomas Burton Karly Turner Phil Jean-Richard Dit Bressel Chelsea Goulton diff --git a/project/project_67/index.html b/project/project_67/index.html index 25c78d6..e9394c1 100644 --- a/project/project_67/index.html +++ b/project/project_67/index.html @@ -1,7 +1,7 @@ -NARPS Open Pipelines - A codebase to study variability of fMRI analysis workflows | Brainhack Global 2023

NARPS Open Pipelines - A codebase to study variability of fMRI analysis workflows

Last updated on -Dec 1, 2023

Title

NARPS Open Pipelines

Leaders

Boris Clénet - R&D Engineer, Empenn Team, INRIA Rennes, France +Dec 7, 2023

Title

NARPS Open Pipelines

Leaders

Boris Clénet - R&D Engineer, Empenn Team, INRIA Rennes, France Mattermost : @bclenet

Collaborators

This project is developed in the Empenn team by Boris Clénet, Elodie Germani, Jérémy Lefort-Besnard and Camille Maumet with contributions by Rémi Gau.

All project contributors are listed in the Credits section of the project !

Brainhack Global 2023 Event

Brainhack Marseille

Project Description

The goal of the NARPS Open Pipelines project is to create a codebase reproducing the 70 pipelines of the NARPS study (Botvinik-Nezer et al., 2020) and share this as an open resource for the community.

We hope this tools will help analysing and understanding variability of fMRI analysis workflows, hence participating in the reproducible research movement.

Find relevant information about how to get started is in the README.md diff --git a/project/project_71/index.html b/project/project_71/index.html index 15a9817..da3b7ab 100644 --- a/project/project_71/index.html +++ b/project/project_71/index.html @@ -1,7 +1,7 @@ -The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI | Brainhack Global 2023

The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI

Last updated on -Dec 6, 2023

Title

The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI

Leaders

  • Lars Kasper @mrikasper
  • Johanna Bayer @likeajumprope

Collaborators

  • Joram Soch @JoramSoch (for MACS integration)

Brainhack Global 2023 Event

BrainHack Toronto

Project Description

TL;DR: Watch the videos on PhysIO +Dec 7, 2023

Title

The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI

Leaders

  • Lars Kasper @mrikasper
  • Johanna Bayer @likeajumprope

Collaborators

  • Joram Soch @JoramSoch (for MACS integration)

Brainhack Global 2023 Event

BrainHack Toronto

Project Description

TL;DR: Watch the videos on PhysIO and MACS to learn about these 2 toolboxes that we are trying to integrate and make more accessible in this Hackathon.

The PhysIO Toolbox offers model-based physiological noise correction for functional MRI (fMRI) data, based on peripheral physiological recordings, such as cardiac and respiratory traces (ECG, pulse oximeter, breathing belt). Major noise models, such as RETROICOR, respiratory volume per time (RVT) or heart-rate variability (HRV) modulations of BOLD are supported.

PhysIO is written in Matlab, but also offered as standalone version via a containerized solution (Neurodesk ) or web-based processing interface (CBRAIN diff --git a/project/project_74/index.html b/project/project_74/index.html index 16623c5..0fbfe0c 100644 --- a/project/project_74/index.html +++ b/project/project_74/index.html @@ -1,5 +1,5 @@ -NeuroLibre reproducible preprints | Brainhack Global 2023

NeuroLibre reproducible preprints

Last updated on Dec 7, 2023

Title

NeuroLibre reproducible preprints

Leaders

Agah Karakuzu, Pierre Bellec

Collaborators

Hao-Ting Wang

Brainhack Global 2023 Event

Brainhack Montreal

Project Description

behapy: A behavioural neuroscience analysis package for Python

Studies using optic fibres to record real-time fluorescent biosensors in-vivo are now commonplace, yet despite an increasing …

 Project URL +MNE +MRtrix +Nipype +SPM +connectome +data visualisation +deep learning +ICA +machine learning +MR methodologies +neural networks +PCA +physiology +reproducible scientific methods +statistical modelling +systems neuroscience

behapy: A behavioural neuroscience analysis package for Python

Studies using optic fibres to record real-time fluorescent biosensors in-vivo are now commonplace, yet despite an increasing …

 Project URL Git level: 1 commit push Git level: 2 branches PRs - + documentation - + Python documentation @@ -79,7 +79,7 @@ pipeline development Jupyter - + systems neuroscience Git level: 0 none @@ -87,24 +87,24 @@ method development visualisation - + Hub australasia aus - + behavioral data management - + statistical modelling

Clustintime: a toolbox for spatio-temporal clustering of fMRI data

  • What are you doing, for whom, and why? This project is a toolbox that allows researchers in neuroimage to apply clustering …

 Project URL Git level: 2 branches PRs - + fMRI - + MRI - + documentation - + Python coding methods @@ -112,31 +112,31 @@ documentation pipeline development - + machine learning method development visualisation - + data visualisation Project - + Hub donostia esp

Launchcontainers: A Python tool for launching containerized analysis on HPC

Launchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program …

 Project URL Git level: 1 commit push Git level: 2 branches PRs - + DWI - + fMRI - + MRI - + documentation - + Python Skills: familiar @@ -146,64 +146,64 @@ documentation BIDS - + reproducible scientific methods Project - + Hub donostia esp

NARPS Open Pipelines - A codebase to study variability of fMRI analysis workflows

The goal of the NARPS Open Pipelines project is to create a codebase reproducing the 70 pipelines of the NARPS study …

 Project URL Git level: 1 commit push Git level: 2 branches PRs - + fMRI - + MRI - + documentation - + Python documentation BIDS - + reproducible scientific methods pipeline development Git level: 0 none - + statistical modelling - + AFNI - + ANTs - + fMRIPrep - + FSL - + Nipype - + SPM - + Datalad

Neurobagel

Neurobagel is a tool ecosystem that allows researchers to easily annotate their dataset (both phenotypic and imaging attributes) …

 Project URL Git level: 1 commit push Git level: 2 branches PRs - + DWI - + fMRI - + MRI - + documentation - + Python Skills: familiar @@ -213,53 +213,53 @@ documentation BIDS - + reproducible scientific methods Git level: 0 none method development - + EEG - + behavioral data management - + Datalad - + Unix command line - + Hub montreal can

NeuroLibre reproducible preprints

  • To bring preprints to life by creating a publishing workflow that can seamlessly integrate narrative and executable content.
  • Our …

 Project URL Git level: 2 branches PRs - + documentation - + Python documentation - + reproducible scientific methods - + html css - + R - + containerization - + Unix command line - + Hub montreal can

phys2CVR: a BIDS-compliant python toolbox to compute cerebrovascular reacitvity mapping

phys2cvr is a python toolbox that aims at offering various approaches to compute cerebrovascular mapping, starting from at least a …

 Project URL Git level: 2 branches PRs - + fMRI - + MRI - + documentation - + Python documentation @@ -267,135 +267,135 @@ BIDS pipeline development - + physiology Project - + Hub donostia esp

Psy2R: Developing an R package for better inference in multivariate statistical analysis

We consistently use massive data sets across neuroscience and psychology. The routine gathering of big data requires that we are …

Git level: 1 commit push - + DWI - + fMRI - + MRI - + documentation coding methods documentation - + reproducible scientific methods method development - + EEG - + Hub australasia aus - + behavioral - + ECOG - + eye tracking - + MEG - + PET - + C++ - + R data management - + statistical modelling

Tedana: TE-dependent analysis

  • What are you doing, for whom, and why?
  • What makes your project special and exciting?
  • How to get started?
  • Where to find key …

 Project URL - + fMRI - + MRI - + documentation - + Python documentation Git level: 0 none - + html css method development - + ICA - + PCA Project - + Hub donostia esp

The evolution of Nipype into Pydra

Nipype is a Python library that provides a uniform interface to existing neuroimaging software and facilitates interaction …

 Project URL Git level: 1 commit push Git level: 2 branches PRs - + DWI - + fMRI - + MRI - + documentation - + Python Skills: familiar documentation - + reproducible scientific methods pipeline development method development - + Git level: 3 continuous integration Skills: comfortable - + AFNI - + ANTs - + DIPY - + FieldTrip - + fMRIPrep - + Freesurfer - + FSL - + MNE - + MRtrix - + Nipype - + SPM

The TAPAS PhysIO Toolbox for Physiological Noise Modeling in fMRI

TL;DR: Watch the videos on PhysIO and MACS to learn about these 2 toolboxes that we are trying to integrate and make more …

 Project URL Git level: 1 commit push - + fMRI - + MRI - + documentation documentation @@ -403,25 +403,25 @@ BIDS pipeline development - + physiology method development visualisation - + data visualisation - + statistical modelling - + SPM - + ECG - + Matlab Skills: expert - + MR methodologies

Why a centralised project submission?

As the Brainhack Global team, we aim to :

  • create a (de)centralized collaborative working platform,
  • facilitate & increase across-site collaborations and interactions,
  • give more visibility to the projects run under Brainhack Global,
  • encourage sharing ideas, experiences and knowledge across parties,
  • to remove barriers and allow contributions by researchers from all origins and disciplines.

Given that many events in this year Brainhack Global might be in part run virtually, a common platform for project submission and listing will allow you diff --git a/sitemap.xml b/sitemap.xml index c5d3a19..a55a7d1 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1 +1 @@ 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