FSL Slice Timing Correction - User Guide | ![]() |
slicetimer
is a pre-processing tool designed to correct for sampling offsets inherent in slice-wise EPI acquisition sequences.
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.
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). |
inputfile.hdr
, then the -r, --repeat
option will not work. If you need to overwrite the existing TR, use avwcreatehd
to regenerate the header file with the new TR value.
--tcustom
option, ensure that you have included the timing offset for the initial slice, even if this is zero.
--ocustom
option, number slices from 1.