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NIDM export in AFNI #4

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cmaumet opened this Issue Sep 14, 2018 · 0 comments

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cmaumet commented Sep 14, 2018

Project Title

Exporting in AFNI fMRI results as NIDM packs

Contributors

Name Position Institute
Camille Maumet Research fellow INRIA, France
Rick Reynolds Computer scientist NIMH
Justin Rajendra Computer scientist NIMH
Gang Chen Mathematical Statistician NIMH

Project Summary

The goal of this project was to make AFNI fMRI results compliant with the NIDM-Results standard.

Project Significance

Providing export to NIDM-Results for AFNI makes it easier for AFNI users to report their fMRI results in compliance with best practices. The generated NIDM packs can be shared on NeuroVault effectively making thresholded and unthresholded maps publicly (or privately) available along with all metadata. NIDM also enhance interoperability across neuroimaging tools (currently: AFNI, SPM, FSL).

Progress Report

Creation of the first-ever AFNI NIDM pack and upload to NeuroVault: https://neurovault.org/collections/ZWGPLHTA/

  1. Brainstorming: updates needed in NIDM to model AFNI fMRI analyses (e.g. voxelwise data scaling, space of the coordinates for the results table, etc.) and possible updates in AFNI to make the export fully automatic (folder formatting, etc.) (all)
  2. Creation of an example dataset, understanding usage for 3dClusterize (RR, CM)
  3. Coding: ClustExp_StatParse.py to export clusters and peaks as JSON (JR), Minimal NIDM export script from a 3dttest++ example (CM). In future stages, the exporter will rely solely on metadata extracted by the ClustExp_StatParse.py routine.

why events like this enable these types of projects?

In person meetings are invaluable to make collaborative projects like this one possible. Exchanging information about AFNI analyses and the NIDM standard.

Project URLs

Any links related to the project, including documentation, created apps, Github repositories, etc.

screen shot 2018-09-14 at 11 45 47

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