<code>slicetimer</code> is a pre-processing tool designed to correct for sampling offsets inherent in slice-wise EPI acquisition sequences.
<ANAME="section2"></A><HR><H2>HOW IT WORKS</H2>
<P>
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.
<P>
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.
<ANAME="section3"></A><HR><H2>USAGE AND OPTIONS</H2>
Compulsory arguments (You MUST set one or more of):<br>
<table>
<tr>
<td><code>-i,--in </code></td>
<td>filename of input timeseries</td>
</tr>
</table>
<p>
Optional arguments (You may optionally specify one or more of):<br>
<table>
<tr>
<td><code>-o, --out </code></td>
<td>specify filename for corrected timeseries</td>
<td>default is <code>timeseries_st</code></td>
</tr>
<tr>
<td><code>-h, --help </code></td>
<td>display options list
</tr>
<tr>
<td><code>-v, --verbose </code></td>
<td>display diagnostic messages</td>
</tr>
<tr>
<td><code>--down </code></td>
<td>use reversed acquistion order (count from the last slice back)</td>
</tr>
<tr>
<td><code>-r, --repeat</code></td>
<td>Specify repeat time (TR)
<td>default 3 s if not set in <code>timeseries.hdr</code></td>
</tr>
<tr>
<td><code>-direction</code></td>
<td>direction of slice acquisition (<code>x=1</code>,<code>y=2</code>,<code>z=3</code>)</td>
<td>default is <code>z</code></td>
</tr>
<tr>
<td><code>--tcustom</code></td>
<td>specify location of a single-column text file containing specific timing offsets for each slice</td>
</tr>
<tr>
<td><code>--ocustom</code></td>
<td>specify location of a single-column text file containing
custom ordering of slices (first slice is referred to as 1 not 0).
</tr>
</table>
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<ANAME="section4"></A><HR><H2>GENERAL ADVICE</H2>
<UL>
<LI>Note that if the TR is already set in <code>inputfile.hdr</code>, then the <code>-r, --repeat</code> option will not work. If you need to overwrite the existing TR, use <code>avwcreatehd</code> to regenerate the header file with the new TR value.
<LI>When using the <code>--tcustom</code> option, ensure that you have included the timing offset for the initial slice, even if this is zero.
<LI>When using the <code>--ocustom</code> option, number slices from 1.
