| AVWUTILS - Miscellaneous Image Utilities
|
|
AVWUTILS is a set of useful command-line utilities which allow the
conversion, processing etc. of Analyze/AVW 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.
The different AVWUTILS programs are:
- avw2ascii - convert AVW to ASCII text file (or files if
data is 4D).
- avwcc - run cross-correlations between every volume in
one 4D data set with every volume in another (for investigating
similarities in ICA outputs).
- avwcomplex - a utility that allows 3D or 4D complex
AVW 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).
- avwcpgeom - copy certain parts of an AVW header (image
dimensions, voxel dimensions, voxel dimensions units string, image
orientation and origin) from one AVW header to another.
- avwcreatehd - 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
commonest are: 1=binary, 2=unsigned char, 4=signed short, 8=signed
int, 16=float).
- avwfill - 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.
- avwhd - report every field of an AVW header.
- avwinterleave - interleave two inputs to form a
combined image.
- avwmaths - simple but powerful program to allow
mathematical manipulation of images.
- avwmerge - concatenate AVW 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
file.
- avwnvols - report how many time points are in the
input 4D data set.
- avwroi - 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
is created), b) extract just some time points from a 4D data set, or
c) control time and space limits to the ROI.
- avwsplit - split a 4D file into lots of 3D files
(eg for inputting to SPM).
- avwstats - report certain summary statistics for an
input 3D/4D image. Of particular value is the "robust intensity range"
which calculates the 2% and 98% percentiles.
- avwval - 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.
- if2avw - convert some Interfile format images to
AVW. This is nowhere near a complete implementation so beware!
Copyright © 2000, University of
Oxford. Written by S. Smith.