Join GitHub today
GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.Sign up
Improving tedana support in afni_proc and fMRIPrep #6
Improving tedana support in
|Elizabeth DuPre (@emdupre)||Graduate Student||Montreal Neurological Institute|
|Rick Reynolds (@afni-rickr)||Senior Computer Scientist||National Institutes of Health|
|Chris Markiewicz (@effigies)||Software Developer||Stanford University|
|Ross Markello (@rmarkello)||Graduate Student||Montreal Neurological Institute|
tedana is a python package for multi-echo EPI denoising. It relies on preprocessed data, and therefore requires integration into larger pipelines like
fMRIPrep. Our goal was to improve this integration and remove the need for duplicated code.
tedana was originally developed in part at the NIH-FMRIF, and it has been supported by the AFNI team for the past several years. This support has lead to widespread adoption, with multiple groups outside of the NIH using and modifying the
tedana code base to suit their particular needs. However, this code has not been fed back to the AFNI code base, and the lack of communication between groups has yielded a significant support burden for the AFNI team. The intention of the
tedana project is to provide a central, maintainable repository for multi-echo EPI denoising, with accompanying documentation and support. By better integrating this new
tedana implementation into
fMRIPrep, we will provide increased user support, standardize calls across systems, and relieve some of the maintenance burden from the AFNI team, all while de-duplicating code.
At Code Convergence, we were able to make significant progress on several initiatives to improve
tedana support in both
afni_proc.py. This was only possible because core maintainers from all of these projects were present in the same room, and we were therefore able to identify issues that might have been missed in silo'ed conversations. Please see Project URLs for a partial listing of code that came out of the event.