Open davidmeunier79 opened 1 year ago
@Brainhack-Marseille
Hi @brainhackorg/project-monitors my project is ready!
We need to test if everything is matching for our own Brainhack-Marseille event, but we need to see how it works after your approval! Thanks
Things look good to me but I am unsure whether this is a project within macapype or something more generic where the aim is to contribute back to pydra or something else. Or maybe I misread it.
@Remi-Gau Indeed it is more than macapype or neuropycon; if people come with shell or matlab scripts the idea would be to help them to build nipype pipeline from it; if people are skilled in nipype already, there is room for working on nipype-> pydra conversion. Does that make sense to you?
yup makes sense to me!
@davidmeunier79
Your project is on the website: https://brainhack.org/global2022/projects/
Title
Automatise your processing pipelines with nipype / pydra
Leaders
David Meunier : Twitter: https://twitter.com/DavidM0579 Mattermost: @david.meunier https://mattermost.brainhack.org/brainhack
Collaborators
To fill at the end
Brainhack Global 2022 Event
Brainhack Marseille
Project Description
Neuroimaging and electrophysiology processing requires many steps, calling different softwares, possibly in different languages (typically, matlab batches or shell scripts).
Nipype has provided an integrative solution, with a sufficient level of complexity to cover most of the needs for writting pipelines in neuroimaging. It is based on the notion workflows, being an orderd succession of nodes, linking inputs and outputs. Nodes can be user-written function (in python), interfaces with existing softwares (e.g. FSL, AFNI or SPM), or even other user-defined sub-workflows.
Nipype is at the base of many widely used docker images, such as fmriprep and qsiprep. And has been extendend for other applications, such as EEG/MEG processing (ephypype), graph analysis in functional connectivity (graphpype) or non-human primate anatomical MRI segmentation (macapype).
Nipype has now achieved a degree of maturity to have become predominant in the community. But some of the limitations still prevails. It has decided in the last years to rewrite the core engine of nipype, to incorporate new functionnalities, such as runnnig containers as one node. The new implementation will be called pydra, and also still in its infancy, we expect it to become a major standard in the community.
Link to project repository/sources
Nipype: https://github.com/nipy/nipype
Pydra: https://github.com/nipype/pydra
Related projects: https://github.com/Macatools/macapype (potentially) https://github.com/neuropycon/ephypype https://github.com/neuropycon/graphpype
Goals for Brainhack Global
In this project, we propose :
For advaced users, We also propose:
Good first issues
Communication channels
https://mattermost.brainhack.org/brainhack/channels/bhg22-marseille-auto-nipype-pydra
Skills
Neuroimaging/electrophysiology processing: 100% Shell Script / Matlab Batch: 75% Python: 50% Nipype: 25%
Onboarding documentation
https://macatools.github.io/macapype/contribute.html
What will participants learn?
Writing easily modifiable and reusable pipeline; Contributing to reproducible science
Data to use
None
Number of collaborators
1
Credit to collaborators
Starting a new pydra-based project will be rewarded as a main contributor to the project, and possibly as an author on a subsequent prospective (methological) article. Working on your pipeline will be rewarded as your own github project.
Image
Type
pipeline_development
Development status
0_concept_no_content
Topic
reproducible_scientific_methods
Tools
Nipype
Programming language
Python
Modalities
fMRI
Git skills
2_branches_PRs
Anything else?
Testing is project template is directly usable on the website BrainHack Marseille 2022, Subject to modification.
Things to do after the project is submitted and ready to review.
Hi @brainhackorg/project-monitors my project is ready!