fMRI Preprocessing

Performs fMRI image preprocessing using FSL suite tools, including:

  • Movement correction (mcflirt)

  • Slicing time correction (slicetimer)

  • Brain Extraction (bet2)

  • Smoothing (susan)

  • Intensity normalization (fslmaths)

  • Pass band filter (fslmaths)

fMRI pre-processed output examples

Input fMRI
Average Corrected fMRI

Required inputs:

  • fMRI: resting-state functional 4D timeseries
    Isotropic resolution recomended
    Must be labeled as 'fMRI' modality"

Minimum input requirements:

  • For optimal result reliability, isotropic resolution is recommended
  • T1 recommended resolution: 1 mm isotropic.
    • T1 minimum reliable resolution: 2mm isotropic.


  • Preferred DICOM to NIfTI conversion tool (drop-down selection)
    The selected tool will be tried first to convert DICOM to NIfTI. If conversion fails, the other options will be tried sequentially until a successful conversion.
      • Mrtrix (Default)
      • bru2nii
      • DCM2nii
      • mcverter
      • diffunpack
  • Skip rs-fMRI preprocessing (checkbox)
    • If checked it converts to NIfTI only (Default unchecked)


  • Images:

    • fmri_corr.nii.gz: preprocessed functional data.

    • fmri_mean.nii.gz: average of all functional volumes.

Typical execution time:

  • 10 minutes

Additional details:

  • None



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