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MRI and PET image formats

Matthew Belmonte matthew at sdsc.edu
Wed Nov 3 05:16:47 EST 1993

trai at tanuki.twics.co.jp writes:

>   I have used Siemens Magnetom(1.5T), and GE Signa Advantage(1.5T).  Both
>of them have simple data structures; each pixel consists of 2 bytes
>expressing pixel value.  The order of the pixels is from the left to the
>right, and from the upper line to the bottom line.

My experience differs somewhat; perhaps the GE format varies across particular
machines or software releases.  FYI, here is a documentation file that I made
up a little over a year ago when I was trying to reverse-engineer formats for
a couple machines:

A GE tape consists of a sequence of small files interspersed with files of size
145408.  The small files contain useless header information and can be ignored.
Each of the large files contains one slice, and these should be in sequence on
the tape in the same order in which they were obtained.  The first 14K (14336)
bytes of each file contains header information -- patient name, institution,
scanning protocol, &c.  For the most part this is in the form of ASCII strings
and should be readily observable just by looking at a dump of the file.
The other 128K of a GE file is a 256x256 image.  No compression is used.  Rows
are stored bottom-to-top and each row is stored left-to-right.  Each pixel is a
2-byte grayscale value which occurs in MSB:LSB (Motorola) order.  In practice
not all sixteen bits are significant, and you can translate to 1-byte pixels
without losing much.  Dividing by four or by eight usually works well for this;
if you want to fine-tune it for a particular image you can experiment.

Siemens format (caution: I have seen a couple tapes from a Siemens machine that
did not follow this format, but the only difference was the size of the header):
Again, there are some small files on the tape that you can treat as garbage.
The ones that you're interested in have 8K of header followed by 128K of image
followed by 2K of tail.  The storage format is similar to GE's, with the
difference that the pixels are stored in LSB:MSB (Intel) order.  Again, in
practice not all sixteen bits are significant.

DISCLAIMER: These formats are the result of reverse-engineering.  My
information comes from my own poking around, not from any official technical
data, so don't treat it as dogma.
Matthew Belmonte	mbelmonte at ucsd.edu
`The Bohemian Kingdom' - Risley Residential College for the Creative and
Performing Arts, Ithaca, New York

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