From 43d2ba75c5eeb772dbd0b416f3c5c308acc81f04 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Thu, 11 Dec 2014 13:00:08 +0000
Subject: [PATCH] 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
Delete:
doc/index.html
---
Makefile | 2 +-
doc/index.html | 86 --------------------------------------------------
2 files changed, 1 insertion(+), 87 deletions(-)
delete mode 100644 doc/index.html
diff --git a/Makefile b/Makefile
index 4359bc6..acfa770 100644
--- a/Makefile
+++ b/Makefile
@@ -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
diff --git a/doc/index.html b/doc/index.html
deleted file mode 100644
index 0c13b8f..0000000
--- a/doc/index.html
+++ /dev/null
@@ -1,86 +0,0 @@
-<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 © 2002, University of
-Oxford. Written by <A
-HREF="http://www.fmrib.ox.ac.uk/~prb/index.html">P. Bannister</A>.</FONT>
-
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-
-</BODY></HTML>
-
--
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