Run presurf_MPRAGEise
MPRAGEising is better than background removal ('denoising')
Optional:
Strip dielectric pads if used now (see PadsOff, needs ANTs)
Run presurf_INV2
Run presurf_UNI
Use the INV2 stripMask to clean up the non-brain parts of the MPRAGEised UNI image.
e.g. fslmaths MPRAGEised.nii -mul stripMask.nii MPRAGEised_stripped.nii
Run recon-all using the MPRAGEised_stripped image
Here is an example of a fully automated segmentation using presurfer + Freesurfer and laminar surfaces:
Run presurf_biascorrect to do just do SPM bias-correction.
Every step produces a sub-directory in the working directory containing all relevant segmentations and masks.
e.g. running presurf_INV2 creates a presurf_INV2 sub-directory