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Commit 43d2ba75 authored by Matthew Webster's avatar Matthew Webster
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This commit was manufactured by cvs2svn to create tag 'FSL6-0-0'. 

Sprout from master 2013-06-21 15:46:13 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'correction for other direction'
Cherrypick from newnew 2014-12-11 13:00:07 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> '2014 Candidate checkin':
    Makefile
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    doc/index.html
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......@@ -7,7 +7,7 @@ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
OBJS = slicetimer.o
LIBS = -lnewimage -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lprob -lm -lutils -lz
LIBS = -lnewimage -lmiscmaths -lNewNifti -lznz -lnewmat -lprob -lm -lutils -lz
XFILES = slicetimer
......
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<HTML><HEAD><link REL="stylesheet" TYPE="text/css" href="../fsl.css"><TITLE>FSL</TITLE></HEAD><BODY><hr><TABLE BORDER=0 WIDTH="100%"><TR><TD ALIGN=CENTER><H1>
FSL Slice Timing Correction
</H1>
User Guide
<TD ALIGN=RIGHT><a href="../index.html"><IMG BORDER=0 SRC="../images/fsl-logo.jpg"></a></TR></TABLE>
<A NAME="section1"></A><HR><H2>INTRODUCTION</H2>
<P>
<code>slicetimer</code> is a pre-processing tool designed to correct for sampling offsets inherent in slice-wise EPI acquisition sequences.
<P>
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.
<p> 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.
<p> If slices were acquired from the top of the brain to the bottom
select the
<b>--down</b> option.
<p> If the slices were acquired with interleaved order (0, 2, 4 ... 1,
3, 5 ...) then choose the
<b>--odd</b> option.
<p>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.
<p>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.
<A NAME="section3"></A><HR><H2>USAGE AND OPTIONS</H2>
<pre>
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 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)
</pre>
<!-- J-Back -->
<p><HR><FONT SIZE=1>Copyright &copy; 2002, University of
Oxford. Written by <A
HREF="http://www.fmrib.ox.ac.uk/~prb/index.html">P. Bannister</A>.</FONT>
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</BODY></HTML>
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