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      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.

      Settings:

      • 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)

      Outputs:

      • 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

      References:

       


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