Title: Pydesperate times call for Pydrastic measures
Project lead: Dorota Jarecka (MM: @dorota) and Chris Markiewicz (T: @effigies, MM: @markiewicz)
Registered Brainhack Global 2020 Event: Montreal
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.
Pydra is a new workflow engine, written from scratch for Nipype 2. Pydra is reaching the maturity needed to justify upgrading workflows from Nipype 1, and it is time to build out the remainder of the ecosystem.
In this hackathon, we will focus on building tasks (interfaces) for neuroimaging tools that can be coordinated by Pydra, and workflows, sequences of tasks that meet real needs in neuroimaging.
If you’re familiar with Nipype 1 and would like to flesh out a set of tasks (e.g., AFNI), we have a tasks template that you can use. If you would rather focus on a workflow, we encourage you to use the niflow manager to begin to create a workflow.
Please read the contribution guide for tips on getting started and our policies on acknowledging contributions.
Data to use: This project is not focused on any specific dataset, but participants are welcome to bring their own data or public data for testing and demonstrations. For MRI-based workflows, we can recommend OpenNeuro ds000114 for different tasks and modalities.
Link to project repository/sources: https://github.com/nipype/pydra
Goals for Brainhack Global 2020:
Good first issues:
Tools/Software/Methods to Use:
Type of project: #documentation, #method_development, #pipeline_development
Project development status: #2_releases_existing
Topic of the projet: #reproducible_scientific_methods, #workflows
Tools used in the project: #Nipype, #AFNI, #ANTs, #BIDS, #Brainstorm, #Datalad, #DIPY, #FieldTrip, #Freesurfer, #FSL, #MNE, #MRtrix, #SPM
Tools skill level required to enter the project (more than one possible): #comfortable, #expert, #familiar
Programming language used in the project: #Python, #containerization, #documentation, #shell_scripting, #Unix_command_line,
Modalities involved in the project (if any): #behavioral, #DWI, #ECG, #ECOG, #EEG, #eye_tracking, #fMRI, #fNIRS, #MEG, #MRI, #PET, #TDCS, #TMS
Git skills required to enter the project (more than one possible): #1_commit_push, #2_branches_PRs, #3_continuous_integration
I added all of the labels I want an associate to my project
Once the issue is submitted, please check items in this list as you add under ‘Additional project info’
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: