Resting State fMRI

Analysis of resting state functional MRI brain data (rs-fMRI) to extract ROI-wise correlation coefficients. This workflow works with the BIDS neuroimaging standard.

The full workflow includes:

  • Conversion of input DICOMs to BIDS structure
  • Various standard fMRI preprocessing steps based on fMRIPrep (such as motion correction, slice timing correction, distortion correction, registration to anatomical space, surface registration, and confound estimation).
  • Postprocessing involving computation of correlation and partial correlation matrices across various regions.
  • ROI-analysis based on segmentation of structural images using either FreeSurfer's recon-all or its compatible, deep learning-based alternative FastSurfer.
  • Visualization of network connectivity across six main large-scale functional networks:
    • Default Mode Network
    • Language Network
    • Both Ventral Attention Networks
    • Salience Network
    • Secondary Visual Network

Report output examples:

Functional connectivity matrix showing correlation coefficient between each pair of ROIs.

Example visualization of functional connectivity between brain regions associated with the Default Mode Network.

Required inputs:

  • fMRI 
    • Resting-state functional 4D time series
    • Isotropic resolution recommended
    • Must be labeled as 'fMRI' modality
  • T1
    • 3D anatomical image
    • Isotropic resolution recommended
    • Must be labelled 'T1' modality

Minimum input requirements:

  • DICOM images

Optional inputs:

  • Gradient field maps
    • Phase image must be tagged 'gfm_phase'
    • Magnitude image must be tagged 'gfm_magnitude'
  • FreeSurfer recon-all segmentation output
    • Segmentation performed on same T1 used as input to the current workflow

Outputs:

  • correlation.csv: Connectivity matrix, with values corresponding to corresponding to correlation coefficient between each pair of ROIs.
  • partial_correlation.csv: Connectivity matrix, with values corresponding to corresponding to partial correlation coefficient between each pair of ROIs. Partial correlation is calculated  by removing the influence of confounding variables. These include 6 motion parameters, 5 compcor components [Behzadi et al. 2007] and the CSF, WM and global signals.
  • report.pdf: report file with results summary.

Typical execution time: ~2 hours

References: