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<H1>The Analyze data format</H1></CENTER>
<P>This page gives some information and links about the the Analyze image data
format. Analyze images are the primary image format used in SPM. SPM also uses
some extensions to the basic format, which are described below.
<P>
<H2>What is Analyze?</H2><A
href="http://www.mrc-cbu.cam.ac.uk/Imaging/analyze.html"
target=display_area>Analyze</A> is an image processing program, written by The
Biomedical Imaging Resource at the Mayo Foundation. The Analyze data format is
used by the Analyze program, and now by a wide variety of other software,
including SPM.
<P>
<H2>The basic Analyze (7.5) format</H2>There are two Analyze formats. One, by
much the more common, is Analyze 7.5. This is the format used by SPM, and
discussed on this page. The other is <A
href="http://www.mayo.edu/bir/Software/Analyze/Analyze1.html">Analyze AVW</A>,
the format used in the latest version of the Analyze program. We won't discuss
AVW format any further, as it not yet used by many programs other than Analyze
AVW itself.
<P>An Analyze (7.5) format image consists of two files, and image and a header
file. If the image is for example named "brain", then the files for that image
will be called "brain.img" and "brain.hdr". The .img file contains the numbers
that make up the information in the image. The .hdr file contains information
about the img file, such as the volume represented by each number in the image
(voxel size) and the number of pixels in the X, Y and Z directions. This header
contains fields of text, floating point, integer and other information.
<P>The SPM99 help system describes the SPM / Analyze image format - see <A
href="http://www.mrc-cbu.cam.ac.uk/Imaging/spm_format.html"
target=display_area>an html version of the SPM99 help on image format</A>.
<P>These links also describe the Analyze format in more detail:
<UL>
<LI><A href="http://www.mayo.edu/bir/PDF/ANALYZE75.pdf">Mayo/Analyze
description of file format</A>.
<LI><A href="http://www.fil.ion.ucl.ac.uk/spm/distrib.html#AzeFmt">SPM/FIL
description of format</A> (this is a less detailed description that the SPM99
help system provides - see above).
<P>However, note that the SPM version of the Analyze format uses a couple of
the header fields in an unconventional way (see below) </P></LI></UL>
<P>
<H2>SPM modifications of the basic analyze format</H2>SPM uses the basic Analyze
7.5 format, but with three modifications / extensions. These are:
<P>
<UL>
<LI>
<H3>The scalefactor</H3>SPM extends the Analyze format by using a scaling
factor for the image from the header.<BR>The purpose of the scale factor is to
allow values in images that cannot be stored using the data type of the .img
file. For example, with an 8 bit image (.img file), all the values in the file
have to be between 0 and 255. SPM extends this, by using the scale factor to
'scale' the values in the img file. Thus, to get actual voxel values for the
image, you read in the numbers from the .img file (0-255 in an 8 bit image),
then multiply these values by the value from the scale factor, from the
header.<BR>The field in the header that SPM uses for the scale factor is
image_dimension.funused1 (see the header field definitions at the <A
href="http://www.mayo.edu/bir/PDF/ANALYZE75.pdf">Mayo/Analyze
site</A>).<BR>The scale factor is useful if the voxel values in the individual
images have meaning either relative to other images, or in some physiological
sense. For example, water activation PET images may have voxel values in
counts per voxel per second, and binding maps calculated for ligands may be
physiological values. These numbers are unlikely to range from 0-255 (which is
the range of an image with values stored in 8 bit), but can be rescaled to
this range by using the scale factor. An alternative would be floating point
images, but these are a) larger and b) not displayable in the earlier (pre
AVW) versions of Analyze.
<P></P>
<LI>
<H3>The image origin</H3>SPM uses one of the Analyze header fields in an
unorthodox way. This is the Originator field (data_history.originator - see <A
href="http://www.mayo.edu/bir/PDF/ANALYZE75.pdf">Mayo/Analyze site</A>). In
the basic format, this is meant to be 10 bytes of text. In SPM, this space is
used to contain three short (two byte) integers. These numbers describe the
current centre or 'Origin' of the image. Specifically, they give the
coordinate of the central voxel, in voxels, in X, then Y then Z. For example,
for images that are aligned to the templates, this Origin field would contain
the coordinates of the voxel nearest to the midline of the Anterior Commisure.
Note that if the Origin is set to 0 0 0, then SPM routines will assume that
the origin is in fact the central voxel of the image.
<P></P>
<LI>
<H3>The .mat file</H3>This is an addition to the Analyze format. It is another
file to add to the imagename.hdr / imagename.img pair - a imagename.mat file.
The file is in matlab .mat file format, and contains information on the
orientation of the image, generated by realignments, coregistration etc. See
the <A href="http://www.mrc-cbu.cam.ac.uk/Imaging/spm_format.html">SPM99 help
on file format</A>, or in rather less detail, see the <A
href="http://www.fil.ion.ucl.ac.uk/spm/distrib.html#AzeFmt">SPM/FIL Analyze
format description</A>, under the heading "The *.mat file". </LI></UL>
<P><I>
<P>Matthew Brett, Chris Rorden 17/6/99</P></I>
<P>
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