Chapter 1
Slice Timing
Contents
1.1 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.1.1 Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.2 Number of Slices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.3 TR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.4 TA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.5 Slice order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.6 Reference Slice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.7 Filename Prefix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Correct differences in image acquisition time between slices. Slice-time corrected files are
prepended with an ’a’.
Note: The sliceorder arg that specifies slice acquisition order is a vector of N numbers, where
N is the number of slices per volume. Each number refers to the position of a slice within the
image file. The order of numbers within the vector is the temporal order in which those slices
were acquired. To check the order of slices within an image file, use the SPM Display option and
move the cross-hairs to a voxel co-ordinate of z=1. This corresponds to a point in the first slice
of the volume.
The function corrects differences in slice acquisition times. This routine is intended to correct
for the staggered order of slice acquisition that is used during echo-planar scanning. The correction
is necessary to make the data on each slice correspond to the same point in time. Without
correction, the data on one slice will represent a point in time as far removed as 1/2 the TR from
an adjacent slice (in the case of an interleaved sequence).
This routine ”shifts” a signal in time to provide an output vector that represents the same
(continuous) signal sampled starting either later or earlier. This is accomplished by a simple shift
of the phase of the sines that make up the signal. Recall that a Fourier transform allows for a
representation of any signal as the linear combination of sinusoids of different frequencies and
phases. Effectively, we will add a constant to the phase of every frequency, shifting the data in
time.
Shifter - This is the filter by which the signal will be convolved to introduce the phase shift.
It is constructed explicitly in the Fourier domain. In the time domain, it may be described as
an impulse (delta function) that has been shifted in time the amount described by TimeShift.
The correction works by lagging (shifting forward) the time-series data on each slice using sinc-
interpolation. This results in each time series having the values that would have been obtained
had the slice been acquired at the same time as the reference slice. To make this clear, consider
a neural event (and ensuing hemodynamic response) that occurs simultaneously on two adjacent
slices. Values from slice ”A” are acquired starting at time zero, simultaneous to the neural event,
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