FSL Slice Timing Correction - User Guide
FSL Slice Timing Correction - User Guide |
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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.
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)