Preprocessing specifically refers to anything that is done to the data prior to computing a standard deviation, but can also include various other things (eg, computing masks). In FS-FAST, these are the preprocessing steps:

* 1. Brain Mask BR * 2. Motion Correction * 3. Slice-Timing Correction * 4. Spatial Smoothing * 5. Intensity Normalization (inorm)

It is not necessary to perform all these stages. Note that B0 correction is not yet avaialble in FS-FAST. Most of these stages are self-explanatory. Brain Mask does a quick segmentation of the brain from the rest of the volume. Intensity normalization is the processes of rescaling all intensity values within a 4D data set so that the in-brain mean is 1000. Intensity normalization is actually done in two stages. The first stage (above) just computes the in-brain mean; the second stage is actually perfromed during the analysis.

The FS-FAST program "preproc-sess" will perform all of these stages. You can run it something like:

["preproc-sess"] -smout fmcsm5 -fwhm 5 -s sessid

There are a lot of things going on "under the hood", so I'll explain each one.-s sessid tells preproc-sess the name of the session as created with unpacksdcmdir. Once it has the session, it can find the raw data in sessid/bold/RRR as f.bhdr (RRR is a run number). It will use the first time point of the first run as a template for both motion correction and brain masking. The brain mask is created using FSL's bet program. The result is stored in bold/masks/brain.bhdr. This is a "binary" mask, ie, each voxel is either 0 (not in the brain) or 1 (in the brain).