Easy fMRI reporting

Publishing fMRI results data

Overview

Teaching: 15 min
Exercises: 0 min
Questions

  • How can I make my fMRI results publically available?

Objectives

  • Learn how to export your results data using NIDM-Results

  • Learn how to publish your results data on NeuroVault

Why publishing fMRI results data?

The most widespread approach to analyze task-based fMRI, often termed “mass univariate”, is to compute one statistical test at each location in the brain.

Best statistical practices for reporting results of hypothesis tests (e.g. SAMPL guidelines) call for reporting of the outcome of each test along with a number of statistic including: the p-value, the type of statistic used, the parametrisation of the test statistic (e.g. degrees of freedom for a T-test) and the statistic value.

For fMRI, complying with theses best practices means publishing one image for each type of statistic to be reported (p-value, statistic value) and a set of metadata describing the testing procedure (type of statistic test, parameters). This lesson describes how to share these data and metadata.

How can fMRI results data be reused?

Image data describing the the results from multiple fMRI studies can be combined to obtain a quantitative synthesis through image-based meta-analysis.

How to publish your fMRI results data?

Gathering the data and metadata

All the data and metadat are usually available to the neuroimaging software package that was used to perform the analysis. But each software package has a different way to store these information. The NIDM-Results specification provides a harmonised representation across neuroimaging software packages in the form of a zip archive that contains all the images and metadata describing the results.

Export your SPM results as a NIDM-Results pack

Install

The latest version of the NIDM exporter in available in the last SPM release.

Usage

  1. In Matlab, open SPM

    spm fmri
  2. Open the Batch Editor by clicking on the Batch button in the SPM12 Menu window
  3. Open the menu SPM > Stats > Results Report (Fig. 1.)
  4. In the batch window (Fig. 2.)
    • Fill in information about the results you are interested in (in particular SPM.mat file, contrast number, threshold, etc.)
    • In Export results, selected New: NIDM (Neuroimaging Data Model)
    • Fill in information about your analysis (Modality, Reference space, Groups, etc.)

More informations at: https://github.com/incf-nidash/nidmresults-spm

Export your FSL results as a NIDM-Results pack

Install

pip install nidmfsl

Usage

nidmfsl [-h] [-g GROUP_NAME NUM_SUBJECTS] [-o OUTPUT_NAME] [-d]
               [-n NIDM_VERSION] [--version]
               feat_dir

More informations at: https://github.com/incf-nidash/nidmresults-fsl

Publication

Results data from fMRI experiments can be shared on NeuroVault. NeuroVault is an online repository that accepts NIDM-Results packs as well as NIfTI images.

Upload your NIDM-Results pack on NeuroVault

Key Points