prestats was previously an omnibus module for the preprocessing of functional MR images. The functionality of prestats is mostly covered by FMRIPREP.

prestats requries a line in the design file that indicates the input image is from FMRIPREP ouput:

# input bold signal is from FMRIPREP output
The prestats outputs are derived directly from the FMRIPREP. The expected outputs include::
  • prefix_preprocessed.nii.gz: Bold signal
  • prefix_referenceVolume.nii.gz: reference volume with skull
  • prefix_referenceVolumeBrain.nii.gz: reference volume without skull
  • prefix_segmenation.nii.gz: segmentation tissues
  • prefix_struct.nii.gz: T1w image
  • prefix_mask.nii.gz: brain mask
  • prefix_fmriconf.tsv: confound regressors from ``FMRIPREP`

All *nii.gz are expected to be have the same voxel size as the input but may have their orientation changed to the FSL standard.

The prestats outputs also consist of Quality Assesmment between structrual and BOLD images::
  • prefix_coregCoverage.txt : Coverage index
  • prefix_coregCrossCorr.txt : Cross correlation
  • prefix_coregDice.txt : Dice index
  • prefix_coregJaccard.txt : Jaccard index