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preprocessMprage (Hallquist pipeline)

preprocessMprage is a prerequisite for Preprocess Functional (Hallquist pipeline). It is analogous to smriprep: skullstrips and MNI-aligns the anatomical/structural T1w image.

Important files include:

  • mprage.nii.gz – input structural image
  • mprage_brain.nii.gz – skull stripped
  • mprage_warpcoef.nii.gz – voxelwise nonlinear warp file for/using fsl's fnirt

QA/QC

The pipeline provides qa_images for quality checking. And can be further inspected using a full nifti viewer like afni.

The most likely failure is during skullstripping.

Failure example

Inspecting further with afni, using $ keypress to toggle the overlay/underlay slider