Chapter 2: Slice-Timing Correction

Unlike a photograph, in which the entire picture is taken in a single moment, an fMRI volume is acquired in slices. Each of these slices takes time to acquire - from tens to hundreds of milliseconds.

The two most commonly used methods for creating volumes are sequential and interleaved slice acquisition. Sequential slice acquisition acquires each adjacent slice consecutively, either bottom-to-top or top-to-bottom. Interleaved slice acquisition acquires every other slice, and then fills in the gaps on the second pass. Both of these methods are illustrated in the video below.


As you’ll see later on, when we model the data at each voxel we assume that all of the slices were acquired simultaneously. To make this assumption valid, the time-series for each slice needs to be shifted back in time by the duration it took to acquire that slice. Sladky et al. (2011) also demonstrated that slice-timing correction can lead to significant increases in statistical power for studies with longer TRs (e.g., 2s or longer), and especially in the dorsal regions of the brain.

Although slice-timing correction seems reasonable, there are some objections:

  1. In general, it is best to not interpolate (i.e., edit) the data unless you need to;
  2. For short TRs (e.g., around 1 second or less), slice-timing correction doesn’t appear to lead to any significant gains in statistical power; and
  3. Many of the problems addressed by slice-timing correction can be resolved by using a temporal derivative in the statistical model (discussed later in the chapter on model fitting).

For now, we will do slice-timing correction, using the first slice as the reference. (This is specified by the -tzero 0 option of the 3dTshift command.) The code for running slice-timing correction will be found in lines 97-100 of your proc script:

foreach run ( $runs )
  3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift \

This will slice-time correct each run with the first slice as a reference. (Keep in mind that in AFNI, everything is indexed starting at 0 - i.e., in this case 0 represents the first slice of the volume). The command also uses an option called -quintic, which resamples each slice using a 5th-degree polynomial. In other words, since we need to replace the values of the voxels within a slice, we can make it more accurate by using information from a larger number of other slices. This does introduce some degree of correlation between the slices, which we will attempt to correct for later by using 3dREMLfit to pre-whiten (i.e., de-correlate) the data.