This page is added to as documentation is written.
Each modality has specific steps, but MRI preprocessing assumes a T1 is available. The T1 defines the native space and the normalization to template space. All modalities are first mapped to native (T1) space, then normalized to template space based on the T1.
T1 preprocessing
The T1 is preprocessed first, as the other modalities are registered to the T1 space.
fMRI preprocessing
bias correction ("m" prefix for mean, "b" prefix for individual fMRI files)
The "m" indicates the images were bias corrected, which (if the option is selected) is done in the SPM "unified" procedure that runs with the segmentation. SPM terms this creating "modulated" images, hence the letter m. Bias correction adjusts for major intensity differences across the fMRI images; I found in one dataset that one side was much darker than the other, which is why I added the option to correct. This darker/brighter is often seen in raw T1 images as brighter or darker spots.
