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Improving tedana support in afni_proc and fMRIPrep #6

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emdupre opened this Issue Sep 14, 2018 · 1 comment

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emdupre commented Sep 14, 2018

Improving tedana support in afni_proc.py and fMRIPrep

Contributors

Name Position Institute
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

Project Summary

tedana is a python package for multi-echo EPI denoising. It relies on preprocessed data, and therefore requires integration into larger pipelines like afni_proc.py and fMRIPrep. Our goal was to improve this integration and remove the need for duplicated code.

Project Significance

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 afni_proc.py and 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.

Progress Report

At Code Convergence, we were able to make significant progress on several initiatives to improve tedana support in both fMRIPrep and 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.

Project URLs

https://tedana.readthedocs.io
poldracklab/fmriprep#1263
poldracklab/fmriprep#1278
ME-ICA/tedana#128

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emdupre Sep 19, 2018

@Shotgunosine this has now been fully updated !

emdupre commented Sep 19, 2018

@Shotgunosine this has now been fully updated !

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