Added more docs and info

doc/index.html

@@ -9,45 +9,81 @@
 <HR>
  
 <P>AVWUTILS is a set of useful command-line utilities which allow the
-conversion, processing etc. of Analyze/AVW format data sets. Many of
+conversion, processing etc. of Analyze/AVW and Nifti format data sets. 
+Many of
 them work on both 3D and 4D data. For each of these programs, type
 just the program name to get the usage help.
 
 <p>The different AVWUTILS programs are:
 <UL>
 
-<LI><b>avw2ascii</b> - convert AVW to ASCII text file (or files if
+<LI><b>avw2ascii</b> - convert image files to ASCII text file (or files if
 data is 4D).
 
 <br><br><LI><b>avwcc</b> - run cross-correlations between every volume in
 one 4D data set with every volume in another (for investigating
 similarities in ICA outputs).
 
+<br><br><LI><b>avwchfiletype</b> - used to change the file type of
+an image (e.g. from ANALYZE_GZ to NIFTI).  The first argument is
+the desired file type (one of ANALYZE, ANALYZE_GZ, NIFTI, NIFTI_GZ,
+NIFTI_PAIR, NIFTI_PAIR_GZ) and the second is the input file.  If
+no third argument is given then the input file is converted in place.
+This in place conversion removes the original files: e.g. for an
+Analyze file called stdimg then
+<kbd>avwchfiletype NIFTI_GZ stdimg</kbd> would replace stdimg.hdr and
+stdimg.img with stdimg.nii.gz.  Note that having multiple copies of
+an image with the same basename and different filetypes (e.g. stdimg.nii.gz
+and stdimg.hdr and stdimg.img) creates many problems for determining
+what images to read, and in general will cause FSL programs to stop.
+
 <br><br><LI><b>avwcomplex</b> - a utility that allows 3D or 4D complex
-AVW files to be split or constructed from corresponding real
+image files to be split or constructed from corresponding real
 components (either Cartesian or polar). The initial flag indicates
 what kind of processing is done.  In addition, two optional arguments
 at the end specify the first and last 3D volumes to be processed when
 the input is 4D (default is to do all volumes).
 
-<br><br><LI><b>avwcpgeom</b> - copy certain parts of an AVW header (image
+<br><br><LI><b>avwcpgeom</b> - copy certain parts of the header 
+information (image
 dimensions, voxel dimensions, voxel dimensions units string, image
-orientation and origin) from one AVW header to another.
-
-<br><br><LI><b>avwcreatehd</b> - create (minimal information) AVW
-header. x/y/z/tsize are image dimensions, x/y/zvoxsize are voxel
-dimensions (eg in mm), tr is time between volumes (for 3D data set to
-0), x/y/zorigin is co-ordinate origin (eg for Talairach space -
-otherwise leave as 0 0 0), datatype is the voxel data type (the
+orientation/origin or qform/sform info) from one image to another.
+Note that only copies from Analyze to Analyze or Nifti to Nifti
+will work properly.  Copying from different files will result in
+loss of information or potentially incorrect settings.
+
+<br><br><LI><b>avwcreatehd</b> - creates a new image header along
+with a zero intensity data image.  There are two forms of input:
+one takes a list of minimal information on the command line, the 
+other takes in an xml-style file, as written by <kbd>avwhd -x</kbd>.
+The information required in the first version is: x/y/z/tsize for 
+image dimensions, x/y/zvoxsize for voxel
+dimensions (eg in mm), tr for time between volumes (for 3D data set to
+0), x/y/zorigin for co-ordinate origin (eg for Talairach space -
+otherwise leave as 0 0 0), datatype for the voxel data type (the
 commonest are: 1=binary, 2=unsigned char, 4=signed short, 8=signed
 int, 16=float).
+Note that this is <b><i>different</i></b> from the previous versions in
+that an entire image is created, and will <b><i>overwrite</i></b> any
+<kbd>.img</kbd> file contents of the same image name.
+
+<br><br><LI><b>avwedithd</b> - allows the header information in
+and image to be edited in a text-based xml-style format (like the
+output of <kbd>avwhd -x</kbd> but with redundant fields removed
+and some help text provided).  Note that
+the default text editor used is pico, but other editors can be
+specified by the second argument.
 
 <br><br><LI><b>avwfill</b> - fill non-brain parts of a 4D data set
 with data copied from inside the brain and adjust time series
 accordingly - useful for programs which need a complete rectangular
 matrix filled with usable but null data.
 
-<br><br><LI><b>avwhd</b> - report every field of an AVW header.
+<br><br><LI><b>avwhd</b> - report every field of an Analyze or
+Nifti header (note that the fields are different although some
+are common, e.g. pixdims).  The option "-x" produces an xml-style
+output which can be used in conjunction with <kbd>avwcreatehd</kbd>.
+
 
 <br><br><LI><b>avwinterleave</b> - interleave two inputs to form a
 combined image.
@@ -55,16 +91,23 @@ combined image.
 <br><br><LI><b>avwmaths</b> - simple but powerful program to allow
 mathematical manipulation of images.
 
-<br><br><LI><b>avwmerge</b> - concatenate AVW files into a single
+<br><br><LI><b>avwmerge</b> - concatenate image files into a single
 output. This concatenation can be in time, or in X, Y or Z. All image
 dimensions (except for the one being concatenated over) must be the
 same in all input images. For example, this can be used to take
-multiple 3D files (eg as output by SPM) and create a single 4D AVW
+multiple 3D files (eg as output by SPM) and create a single 4D image
 file.
 
 <br><br><LI><b>avwnvols</b> - report how many time points are in the
 input 4D data set.
 
+<br><br><LI><b>avworient</b> - reports or sets the left-right
+orientation information in a file.  Note that only in Nifti files
+can the orientation be changed - Analyze files are <i>always treated
+as <b>radiological</b></i>.  Note that this command does not
+change the data storage at all - only the orientation information in
+the header.
+
 <br><br><LI><b>avwroi</b> - extract region of interest (ROI) from an
 image. You can a) take a 3D ROI from a 3D data set (or if it is
 4D, the same ROI is taken from each time point and a new 4D data set
@@ -78,9 +121,29 @@ c) control time and space limits to the ROI.
 input 3D/4D image. Of particular value is the "robust intensity range"
 which calculates the 2% and 98% percentiles.
 
+<br><br><LI><b>avwstats++</b> - just like <kbd>avwstats</kbd> but
+can also calculate percentiles (e.g. <kbd>p 50</kbd> gives the median),
+and the centre of gravity.  In addition, it can take an aribitrary mask
+as input so that statistics are only calculated within the mask.
+
+<br><br><LI><b>avwswapdim</b> - re-orders the data storage to permit
+changes between axial, saggital and coronal slicing.  It can also
+be used to swap the left-right order of the data, but <i>will not
+change the left-right orientation information in the header</i>.
+Therefore after swapping left-right (e.g. using <kbd>-x y z</kbd>
+as arguments) the viewed image will be different.  If the header
+information is also swapped (by using <kbd>avworient</kbd>) then
+the image will display as it originally did, although the data
+will be stored in a different order.  This command is recommended
+for changing neurologically-ordered data into radiologically-ordered
+data.
+
 <br><br><LI><b>avwval</b> - report a particular parameter (given a
-particular keyword eg "dim4") from an AVW header. To see the list of
-keywords run avwhd on the header and look at the first column.
+particular keyword eg "dim4") from an image header. To see the list of
+keywords run <kbd>avwhd</kbd> on the header and look at the first column.
+
+<p>
+<hr>
 
 <br><br><LI><b>avwfixfloat</b> - sets all non-finite (NaN, Inf) values
 and very small values (<1e-37) to zero, which helps avoid some floating
@@ -88,14 +151,14 @@ point errors on Alpha machines.  Note that this is only works for volumes
 with data type = float.
 
 <br><br><LI><b>if2avw</b> - convert some Interfile format images to
-AVW. This is nowhere near a complete implementation so beware!
+Analyze or Nifti. This is nowhere near a complete implementation so beware!
 
 </UL>
 
 
-<p><HR><FONT SIZE=1>Copyright &copy; 2000, University of
+<p><HR><FONT SIZE=1>Copyright &copy; 2000-2004, University of
 Oxford. Written by <A
-HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A>.</FONT>
+HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A> and M. Jenkinson.</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>

fsledithd

@@ -37,7 +37,6 @@ tmpbase2=`${FSLDIR}/bin/tmpnam`;
 echo "# AVWEDITHD" > ${tmpbase}
 echo "# This text file contains the header information for an Analyze or Nifti file" >> ${tmpbase}
 echo "# Simply edit this file then save it and the header will be regenerated" >> ${tmpbase}
-echo "#   (note: if this editor is vi and you don't know it, quit by typing, in order, ESC Z Z )" >> ${tmpbase}
 echo "# All lines starting with the hash (#) character, like this line, will be ignored" >> ${tmpbase}
 echo "# Ensure that all lines intended to set values take the form: name = 'value' " >> ${tmpbase}
 echo "# Note that if the file is Analyze then many settings will be ignored" >> ${tmpbase}
@@ -72,3 +71,4 @@ cat ${tmpbase} | grep -v '^[ 	]*#' | grep -v '^[ 	]*$' > ${tmpbase2}
 ${FSLDIR}/bin/avwcreatehd ${tmpbase2} $1
 
 /bin/rm ${tmpbase} ${tmpbase2}
+