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.


HOW IT WORKS

Each voxel timecourse is processed in parallel and intensities are corrected 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 kernel is applied to each timecourse to calculate the interpolated values. Once the timecourse corresponding to ever voxel within the data has been corrected, the data set is reconstructed and output as a standard AVW 4D file.


USAGE AND OPTIONS

slicetimer -i <timeseries> [-o corrected_timeseries] [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 specify filename for corrected timeseries default is timeseries_st
-h, --help display options list
-v, --verbose display diagnostic messages
--down use reversed acquistion order (count from the last slice back)
-r, --repeat Specify repeat time (TR) default 3 s if not set in timeseries.hdr
-direction direction of slice acquisition (x=1,y=2,z=3) default is z
--tcustom specify location of a single-column text file containing specific timing offsets for each slice
--ocustom specify location of a single-column text file containing custom ordering of slices (first slice is referred to as 1 not 0).


GENERAL ADVICE


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