FSL

# FSL Slice Timing Correction User Guide |

## INTRODUCTION

`slicetimer` is a pre-processing tool designed to correct for sampling offsets inherent in slice-wise EPI acquisition sequences.

Each voxel's timecourse is processed independently and intensities are shifted in time so that they reflect the interpolated value of the signal at a common reference timepoint for all voxels, providing an instantaneous `snapshot' of the data, rather than a staggered sample throughout each volume. Sinc interpolation with a Hanning windowing kernel is applied to each timecourse to calculate the interpolated values.

It is necessary to know in what order the slices were acquired and set the appropriate option. The default correction is appropriate if slices were acquired from the bottom of the brain.

If slices were acquired from the top of the brain to the bottom select the --down option.

If the slices were acquired with interleaved order (0, 2, 4 ... 1, 3, 5 ...) then choose the --odd option.

If slices were not acquired in regular order you will need to use a slice order file or a slice timings file. If a slice order file is to be used, create a text file with a single number on each line, where the first line states which slice was acquired first, the second line states which slice was acquired second, etc. The first slice is numbered 1 not 0.

If a slice timings file is to be used, put one value (ie for each slice) on each line of a text file. The units are in TRs, with 0.5 corresponding to no shift. Therefore a sensible range of values will be between 0 and 1.

## USAGE AND OPTIONS

    slicetimer -i  [-o ] [options]

    Compulsory arguments (You MUST set one or more of):
            -i,--in filename of input timeseries

    Optional arguments (You may optionally specify one or more of):
            -o,--out        filename of output timeseries
            -h,--help       display this message
            -v,--verbose    switch on diagnostic messages
            --down  reverse slice indexing
            -r,--repeat     Specify TR of data - default is 3s
            -d,--direction  direction of slice acquisition (x=1,y=2,z=3) - default is z
            --odd   use interleaved acquisition
            --tcustom       filename of single-column custom interleave timing file
            --ocustom       filename of single-column custom interleave order file (first slice is referred to as 1 not 0)

Copyright © 2002, University of Oxford. Written by P. Bannister.