Medical Image Format FAQ, Part 3/8
David A. Clunie
Posting-Frequency: monthly
Last-modified: Sun Dec 21 09:16:34 EST 2003
Version: 4.26
3. Proprietary Formats
3.1 Proprietary Formats - General Information
3.1.1 SPI (Standard Product Interconnect)
Used for files exported from:
- Siemens Somatom Plus - Siemens Magnetom Impact - Siemens
Magnetom SP - Siemens Magnetom Vision - Philips Gyroscan S5 - ?
what else ?
SPI is a standard based on the old ACR/NEMA 1 standard, devised I
gather by Siemens and Philips, for use in a PACS environment. Who
currently maintains it and whether or not Sienet PACS systems are
based on it, I am not certain. Many machines in the workplace use
it in some shape or form, or can export files in SPI format. I
gather it has been around since 1987 or so, but I do not yet have
access to the reference documents, nor permission to disclose
their contents, so much of the following is guess work or hearsay
from Usenet.
Like the ACR/NEMA standard, SPI is designed to define
interconnections between pieces of equipment from the physical
level through to the application level. Where appropriate it
utilized relevant parts of ACR/NEMA. Unlike ACR/NEMA, I gather
that SPI is aware of the concept of networks, objects containing
information, the need to uniquely identify instances of objects,
and defines an offline file format. Thus in many ways it sounds
like the missing link between ACR/NEMA 2.0 and DICOM 3.0.
SPI makes use of ACR/NEMA data elements and groups, and in
addition provides "shadow" private odd-numbered groups as dictated
by the ACR/NEMA standard for the purpose of storing additional
items of information, including a means of uniquely identifying
objects, as well as allowing for enumerated values for elements
beyond those defined by ACR/NEMA. SPI also defines a byte order
for offline storage of data streams. Integers are stored in
little endian format (least significant byte first).
The private groups mechanism works as follows. For each odd
numbered group (other than 0x0001,0x0003,0x0005,0x0007 and
0xffff), the elements 0x00nn in the range 0x0010 through 0x00ff
contain a single valued string identification code that identifies
the creator of the range of elements 0xnn00 through 0xnnff. Neat
eh ? For example:
(0x0009,0x0010) PrivateCreatorDataElement (0x0009,0x0011)
PrivateCreatorDataElement ... (0x0009,0x1000) DavidElement1
(0x0009,0x1001) DavidElement2 ... (0x0009,0x1100) HarryElement1
(0x0009,0x1101) HarryElement2
You get the idea. The nice thing about this scheme is that each
creator dictionary considers its elements numbered from 0x0000,
but these will be remapped to a block of elements depending on
exactly which PrivateCreatorDataElement is used in the particular
data set. Hence multiple groups from different creators can
co-exist happily in the same data set, and vary in position
between data sets.
Note that the group number IS taken into consideration ... a
private element with the same element offset and the same creator
will have a different meaning depending on which group it is in.
SPI uses this concept extensively and defines a large dictionary
with different creators with convoluted names for different
modalities and PACS operations. A few sample elements are
described here. Particularly important are those elements for
purposes that were not envisaged when ACR/NEMA 1 was written, but
are necessary to create valid DICOM 3 data sets. Such things as
FlipAngle for MR scans for example. Note that the SPI UID is not
the same as a DICOM UID, but presumably it is unique ! Note also
that the creator of "SPI RELEASE 1" is the same as "SPI Release 1"
and "SPI" ... presumably someone messed up between machines or
modalities or manufacturers. For a more extensive SPI data
dictionary see the DICOM conversion tools. The value
representation fields are shown here using the modern DICOM
equivalents rather than the older, less specific ACR/NEMA names.
The "owner" is what is used as the string value of the
PrivateCreatorDataElement when a range of elements in a group is
claimed.
Element Owner Name VR VM
(0009,0010) SPI Comments LO 1 (0009,0015) SPI UID LO 1 (0009,0010) SIEMENS MED
RecognitionCode LO 1
(0011,0010) SPI RELEASE 1 Organ LO 1 (0011,0015) SPI RELEASE 1 AllergyIndication
LO 1 (0011,0020) SPI RELEASE 1 Pregnancy LO 1 (0011,0010) SIEMENS CM VA0 CMS
RegistrationDate DA 1 (0011,0011) SIEMENS CM VA0 CMS RegistrationTime TM 1
(0011,0023) SIEMENS CM VA0 CMS UsedPatientWeight IS 1
(0013,0020) SIEMENS CM VA0 CMS PatientName LO 1 (0013,0022) SIEMENS CM VA0 CMS
PatientId LO 1 (0013,0030) SIEMENS CM VA0 CMS PatientBirthdate LO 1 (0013,0031)
SIEMENS CM VA0 CMS PatientWeight DS 1 (0013,0035) SIEMENS CM VA0 CMS PatientSex
LO 1 (0013,0040) SIEMENS CM VA0 CMS ProcedureDescription LO 1 (0013,0042)
SIEMENS CM VA0 CMS RestDirection LO 1 (0013,0044) SIEMENS CM VA0 CMS
PatientPosition LO 1
(0019,0010) SIEMENS CM VA0 CMS NetFrequency DS 1 (0019,0011) SIEMENS CM VA0 ACQU
SequenceFileName LO 1 (0019,0021) SIEMENS CT VA0 GEN Exposure DS 1 (0019,0026)
SIEMENS CT VA0 GEN GeneratorVoltage DS 1 (0019,0050) SIEMENS MR VA0 GEN
NumberOfAverages IS 1 (0019,0060) SIEMENS MR VA0 GEN FlipAngle DS 1 (0019,0012)
SIEMENS MR VA0 COAD MagneticFieldStrength DS 1
(0021,0010) SIEMENS MED Zoom DS 1 (0021,0011) SIEMENS MED Target DS 2
(0021,0020) SIEMENS CM VA0 CMS FoV DS 2 (0021,0060) SIEMENS CM VA0 CMS
ImagePosition DS 3 (0021,0061) SIEMENS CM VA0 CMS ImageNormal DS 3 (0021,006a)
SIEMENS CM VA0 CMS ImageRow DS 3 (0021,006b) SIEMENS CM VA0 CMS ImageColumn DS 3
(0021,0039) SIEMENS MR VA0 GEN SlabThickness DS 1 (0021,0070) SIEMENS MR VA0 GEN
NumberOfEchoes IS 1
3.1.2 Siemens - Features common to multiple families
The Numaris (MRI) and Somaris (CT) software contains certain
common features, especially when running on common platforms.
This is particularly true of more recent versions that are Sparc
and SunOS based rather than the older Vax/VMS systems .
3.1.2.1 Siemens Vax/VMS
Under construction.
3.1.2.2 Siemens Sparc SunOS
This information is derived mostly from some recent
experiments with Numaris VB21B on an Open and Somaris on
an AR-C. There is a lot of useful information to be found
in the System Manual for both families, not to mention the
configuration release notes. Both use bog standard Sun OS
4.1.x, and tend to keep the platform/application specific
information in the /usr/appl tree. The user interface is
standard OpenWindows.
3.1.2.2.1 Starting up
This will become apparent when the system is started up.
The normal SunOS boot procedure is observed. On somaris,
the system automatically loads Open Windows and followed
by the Somaris application. On Numaris one logs in as the
"mr" user, usually without any password, and gets
OpenWindows and the Numaris application. Interrupting
this process will be described later.
3.1.2.2.2 Getting a console
The first step in exploring the system is getting a
console. On Numaris this is easy. Running all the way
down the right hand side of the screen is an information
area from the Numaris application. About a third of the
way down the edge, a little grayed out icon is visible.
Clicking or dragging on this will expose the fact that
this is an iconified console window. On Somaris, the
console is still iconified but completely hidden by the
right information area. The trick to grabbing this is to
do a System/End (menu with right mouse button down) and
select Application and Restart, which brings the
application and the OpenWindows down and back up again.
While this is happening you can see the iconified console
and drag it into the middle of the screen, where you can
open it later.
While on the subject of System/End, the various options
are permuations of normal commands like logout, halt or
shutdown.
Once one has a Unix prompt one can explore the system, and
create directories in which to save exported images. The
Numaris manual's example suggested /usr/appl/external as a
place to store exported files. On Numaris this already
exists and is empty. On Somaris it doesn't but the normal
user has the permission to create it with a "mkdir
/usr/appl/external". The normal commands like telnet and
ftp are available if one wants to use these to go outward
bound on the network, if it is configured (which will be
discussed later).
3.1.2.2.3 Native images
Images are stored in native form in /usr/appl/data/disk1,
at least on the systems that I have examined. They are
stored one image per file, and named something like
nnn-ss-iii.ima, where nnn is some sequential number that
pertains to the patient (or instance of the examination
... I am not sure), ss is the series number (always 1 on
Somaris), and iii is the sequential image number within
nnn. The hard part is figuring out what nnn is for the
patient you want ... this number is not displayed in the
normal Patient Select dialogs or anywhere else I can find.
Counting back from the latest patient and comparing the
highest value of iii seems to be a crude but effective
approach.
The native images are stored in the usual Siemens style,
with a binary header of fixed length (that varies from
product to product in length and layout) and trailing
uncompressed image pixel data. The specifics where known
are described elsewhere.
3.1.2.2.4 Exporting images
On any of these products one can use the System/External
Data menu option to bring up a dialog with Import or
Export choices. Select Export, enter /usr/appl/external
or whatever as the destination, and choose the image
numbers (eg. "1-6,10,22-24" is quite acceptable) and they
will be written where you asked. The patient name must be
exactly as it is registered. The catch is that the
exported SPI files will be named with the patient's name
and the current date and time of export, not the time of
acquisition or reconstruction or whatever, so sorting
through these to determine what they are is a pain. The
form of the date and time stamp in the name is
"yyyymmddhhmmssff".
3.1.2.2.5 Physical connection
So you know where the images are ... how do you get them
off. One way is by ethernet connection. One doesn't have
to have the PACSNet or DICOM option to be able to connect
to the network. If you haven't paid for the PAL that
provides hardware protection for these functions, it
doesn't mean that the ethernet software in Sun OS and the
ethernet port on the Sparc host is not live. During
installation of the Somaris or Numaris software the
Siemens Field Engineer can configure the interface with a
IP address of your choice (it defaults to 1.0.0.1 under
Numaris, and the le0 interface is not configured by
default under Numaris).
If the Siemens FE is unfamiliar with the procedure tell
them to use the "install" login, choose SSC (Site Specific
Configuration) then RC (Reset host Configuration),
accepting the defaults until you get to "Internet
Address". If you know the "install" password (or can
change it as root) you can do this yourself. I don't
think the additional layer of Siemens password protection
applies to this particular tool, though there are many you
won't be able to run.
If you are really desperate you can gain root access and
manually configure the SunOS network configuration without
using the Siemens tool, but you need to be pretty familiar
with SunOS to do this. You need to put in a real IP
address in /etc/hosts, create an /etc/hostname.le0, and if
necessary set up /etc/netmasks if the default is not
appropriate. I tried this and it works but it somehow
messed up camera communications, so doing it with the
Siemens FE is probably better. Don't forget to back up
the critical files first just in case.
The standalone configuration on the AR/C had just the
loopback address (127.0.0.1) in /etc/hosts and no
/etc/hostname.le0.
The physical ethernet connector is normally unused, and is
located on the Sparc host board and is the usual AUI
connector (ie. you need an AUI to 10BaseT or whatever
transceiver). On the AR/C I tested it was located under
the desktop (ie. lift the desktop off, and then the metal
cover), sticking up on the left hand side. On the
Magnetom Open it was in the computer room in the cabinet
with the host processor at the bottom on the left hand
side. In this installation it was connected to a lead
going to a breakout panel on the top cover of the cabinet.
This is unused so just disconnect it and plugin your own.
3.1.2.2.6 Archive devices
Another way to get the images off is to just use the QIC
streaming tape drive. This is probably still installed in
older machines, but the newer software is being
distributed on CD-ROM so the tape drive is being pulled
and replaced with a CD. It is probably still in the
maintenence closet though and would be easy to swap back
in. No configuration is necessary. It is accessed as
usual as /dev/rst0 and its rewinding and non-rewinding
variants, and one can just tar image files off to it.
Very handy. No messing with wierd Pioneer WORM's and
MOD's !
The drive is physically located on the front of the
processor box in the desk models and in the host processor
cabinet beside the optical drive in the computer room in
the larger installations.
Speaking of WORM's and MOD's, they are the same unreadable
media as used by GE, but of course have a different
filesystem. When used as archive devices these are not
the standard unix file system, and you will not see any
evidence of a mounted device doing a "mount" or "df", even
though when you stick one in the drive the application
automatically detects it and mounts it. It is said in the
release notes that one can actually format and mount one
of these as a unix filesystem instead (the MOD at least)
but I don't know how to do it, and haven't discovered, not
possessing one of them there Pioneer drives to read one
on.
3.1.2.2.7 Becoming root
If you thought you could mess up a perfectly good scanner
already, try becoming root. Why would one need to do this
? To manually reconfigure the network, to change
passwords for critical logins like install, to create your
own login some place clean and safe, etc. Since this is
standard SunOS, the usual principles apply ... first try
rebooting in single user mode. Do this with a System/End
choosing System/Norestart and you will get a boot prompt.
Type "b -s" and it comes up in single user mode, allowing
you to mess with /etc all you like as root.
If this mode has been password protected (and one can do
this by removing "secure" from "console" in /etc/ttytab
... see "man 5 ttytab") then one is not out of luck yet.
Now you have to put a SunOS boot disk in the CDROM drive
(or plugin an external CDROM drive) and boot SunOS
mini-root, then mount /dev/sd0 as /mount and you are in
business. (If you don't have a SunOS CDROM then you
probably shouldn't be doing this kind of thing in the
first place).
3.1.2.2.8 Reset
If you are messing about in SunOS, periodically the
Somatom application will get out of sync with the new
reality you have created and will complain that an
Init/Reset is necessary ... well, do an Init/Reset. I
have forgotten exactly where it is in the menus, whether
under System or Measurement. It is documented in the
system manual and seems harmless.
3.2 CT - Proprietary Formats
3.2.1 General Electric CT
Now we get to the meaty part. After years of being faced with the
problem of either a) hours of detective work, or b) tediously
tracking down the name of the responsible person and exercising a
non-disclosure agreement, this is now no longer necessary, as
General Electric are making their image format description
documents freely available. For details see the GEMS image format
information contacts section later on. In the meantime, both for
historical completeness, educational purposes, and for those who
can't wait for document to come in the mail, a summary of the
relevant formats and decompression algorithms is provided here.
3.2.1.1 GE CT 9800
References (see the GEMS image format information contacts
section):
- 46-021855 CT 9800 Image Data Format
3.2.1.1.1 GE CT 9800 Image data
- "block format" header - perimeter encoding -
optional DPCM compression - Data General host
(various) - RDOS (yuck !)
Almost everyone in this field has at some stage
encountered the dreaded CT 9800 format. The
world is divided into two groups of people ...
those who have seen the documents or the
critical piece of code in another program or
have been given a handy hint, and those who will
never figure out the format themselves.
Essentially the format fits into the "block
format" described earlier, with pointers to each
of the major header components. Rarely, if
ever, does one encounter a file that doesn't
have the same size blocks in the same place, so
most people treat it as a fixed layout. I
believe that reformatted images may have another
header stored in there, but I have never tested
for it.
The data itself is stored in one of two forms
depending on whether compression is selected or
not during archival. In the uncompressed form,
a type of perimeter encoding is used (see later
section) in which for an essentially circular
object, the outer parts of a rectangular image
are discarded (and expected to be filled in with
a background pixel value during reconstitution
of the image). In the case of the CT9800 then,
the image pixel data is interpreted using a map,
which contains an entry for each row of the
image (either 256, 320 or 512 entries) which
specifies the length of the row that is actually
stored, centered about the midline of the image.
This obviously saves a lot of space.
If compression is selected on one of the later
model machines, then a form of Differential
Pulse Code Modulation is used, in which
advantage is taken of the fact that not all the
bits of a 16 bit word are need to store a CT
value. I gather only 12 bits of data are
actually significant, but one can theoretically
represent 15 using this scheme. Essentially,
the first 16 bit word is read and used as is.
Then another byte is read. If its most
significant bit is set, then the remaining 7
bits represent a signed difference value
relative to the previous pixel. If its most
significant bit is not set, then the difference
must have exceeded the range of 7 bits, and
hence the next byte is read to complete a valid
16 bit word (15 bits really) which is the actual
pixel value. The really neat thing about this
scheme is that the same algorithm can be used
for compressed or uncompressed data as an
uncompressed stream of words will never have the
most significant bit set !
The following piece of C++ code pulled out of a
CT9800 to DICOM translator will give you the
general idea. Note that the perimeter encoding
map has already been read in. Note in
particular the need to deal with sign extension
of the difference value. Also note that the
code doesn't handle the first pixel specially
because its high bit will not be set.
static void copy9800image(ifstream& instream,DC3ofstream& outstream,
Uint16 resolution,Uint16 *map)
{
unsigned i; Int16 last_pixel;
last_pixel=0; for (i=0; i<resolution; ++i) {
unsigned line = map[i]; unsigned start = resolution/2-line;
unsigned end = start+line*2; unsigned j;
// Pad the first "empty" part of the line ... for (j=0;
j<start; j++) outstream.write16(0);
// Copy the middle of the line (compressed or uncompressed)
while (start<end) {
unsigned char byte; instream.read(&byte,1); if
(!instream) break; if (byte & 0x80) {
signed char delta; if (byte & 0x40) {
delta=byte;
} else {
delta=byte & 0x3f;
} last_pixel+=delta;
} else {
last_pixel=byte << 8; instream.read(&byte,1); if
(!instream) break; last_pixel+=byte;
} outstream.write16((Uint16)last_pixel & 0x0fff);
++start;
}
// Pad the last "empty" part of the line ... for (j=end;
j<resolution; j++) outstream.write16(0);
}
}
What about the rest of the header information
and where is this map stored anyway ? Well, the
file is described as a series of 256 by 16 bit
word blocks, blocks numbered from 0, words
numbered from 1, integers are 16 bit words, as
follows:
block 0 - global header
word 34 - Int - pointer to global header word 35 - Int - pointer
to exam header word 36 - Int - pointer to image header word 37 -
Int - pointer to image header2 word 38 - Int - pointer to image
map word 39 - Int - pointer to image data word 40 - Int - number
of blocks in global header word 41 - Int - number of blocks in
exam header word 42 - Int - number of blocks in image header word
43 - Int - number of blocks in image header2 word 44 - Int -
number of blocks in image map word 45 - Int - number of blocks in
image data
Now almost always the layout is as follows, for
non-reformatted images:
block 0 - global header block 1 - exam header block 2 - image header
block 3 - image header 2 block 4 - image map block 6 - image data
For reformatted images the layout is said to be
different, but I have never seen a description
of the contents of the so-called "arrange
header", nor do I know where in the global
header the pointer and length are stored:
block 0 - global header block 1 - exam header block 2 - image header
block 3 - image header 2 block 4 - arrange header block 9 - image map
block 11 - image data
Some of the more important contents of the
various headers are listed here. For more
complete information get the documents from GE
or study any one of a number of programs kicking
around to dump the header of this kind of file
(see sources later). Integers are 16 bit words,
ascii strings are Fortran style specifications
with two characters per word, and reals are 4
bytes long (see Host machines - Data General):
block 0 - global header
word 17-23 - 7A2 - file name
block 1 - exam header
word 4 - Int - exam number word 5-11 - 7A2 - exam number word
12-17 - 6A2 - patient id word 18-32 - 15A2 - patient name
block 2 - image header
word 11 - Int - position (study) number word 13 - Int - group
type (2=scout,3=standard,4=dynamic) word 14 - Int - group number
word 47 - Int - scan number word 48 - Int - image number word 50
- Int - patient orientation (1=head first,2=feet) word 51 - Int -
AP orientation (1=prone,2=sup,3=lt,4=rt) word 55 - Int - contrast
(0=no,1=yes) word 93-94 - Real - gantry tilt word 95-96 - Real -
table height mm word 97-98 - Real - axial table location mm word
124 - Int - image size (256,320,512) NOT FOR SCOUTS word 132 -
Int - detectors/view - width for scouts word 137 - Int -
compressed views/scan - height for scouts word 144-145 - Real - X
diameter of recon mm word 146-147 - Real - Y diameter of recon mm
word 155-156 - Real - magnification factor word 157-158 - Real -
X center word 159-160 - Real - Y center word 175 - Int - image
map used (1=yes,2=no) word 218 - Int - file type
(1=prospective,2=scout,
3=retrospective,4=segmented, 5=screen
save,6=plot)
word 219 - Int - data range (number of bits) word 236 - Int -
scout orientation (0=ap,1=lateral)
(the 9800 rotates the scout magically)
It is important to check the filetype and image
map used entries, particularly if trying to read
scouts rather just prospective images. If the
map is not in use, it is filled with zeroes and
hence if the flag is not checked a simplistic
demapping algorithm will fail. Furthermore the
number of rows and columns in the image is not
specified as such. For prospective images, the
imagesize field is valid for both (images are
square). For scouts, one must use the
detectors/view field for the width and the
compressed views/scan field as the height.
The filename entry is quite useful. Therein is
stored the RDOS filename of the image, which
follows the following convention:
s = originating scan station id eeeee = exam number pp = prs number
(position related set) dd = image number tt = file type
YP = prospective YV = scout YR = retrospective YG = segmented
recon YS = screen save YL = plot YF = reformatted
eg. B038500165.YP
Having said this, my GE 9800 stores its scouts
on tape at least with no file extension at all,
rather than the .YV that it is supposed to use.
3.2.1.1.2 GE CT 9800 Tape format
Probably more CT images have been exchanged for
clinical and research purposes using GE 9800
9-track magnetic tapes than any other means.
These things are just ubiquitous, particularly
considering the proliferation of services
providing 3D reconstruction and fabrication a
few years ago. Fortunately the format is easy
to deal with. The tapes are produced on a
primitive DG tape drive and hence are never more
than 1600bpi. The first thing on the tape is a
directory consisting of two 4096 word (8192
byte) records, then two EOF marks, then 20" of
blank tape (because the directory keeps getting
updated) followed by image files each separated
by an EOF mark and finally an additional EOF
mark after the last file.
I won't describe the tape directory format here
unless someone specifically asks for it, though
it is very simple. I usually just read
everything on the tape and sort the files out
later. Remember that their filenames are stored
in the global header.
Don't forget to set the input magnetic tape
record size to 8192 bytes when you are copying
these files. If you don't do this some systems
quietly truncate each record to some default
size. It took me a week to figure out why my
files were screwed up the first time I tried
this on a DG under AOS/VS (I was desperate and
using a networked Signa to read files off a
non-networked 9800).
A simple script to read an entire tape from a
SCSI tape drive /dev/nrst1 under SunOS, which
will peek in each image file to extract the
correct filename (simpler than trying to
decipher the directory) looks like this:
#!/bin/sh
echo "Rewinding" mt -f /dev/nrst1 rewind
echo "Extracting directory ..." dd if=/dev/nrst1 ibs=8192 of=TAPEDIR
while dd if=/dev/nrst1 ibs=8192 of=tape.tmp do
name=`dd if=tape.tmp ibs=16 skip=2 count=1 2>/dev/null` if [ -z "$name"
]; then break; fi mv tape.tmp $name echo "Extracted $name"
done
echo "Rewinding" mt -f /dev/nrst1 rewind echo "Finished"
3.2.1.1.2 GE CT 9800 Raw data MR
No idea about this one ... I have never had the
need or seen any documention. Anyone who does
or has please fill in this space.
3.2.1.2 GE CT Advantage - Genesis
References (see the GEMS image format information contacts
section):
- 46-021861 Image Data Format - 46-021863
Optical Disk Raw Partition - 46-021864 Image
Extract Tool - 46-021865 DAT Archive Format
General Electric now uses the same Sun based architecture
for its Advantage CT and Signa 5X MR family, referred to
as Genesis, and hence the general details of this scheme
will be discussed under the GE MR Signa 5.x - Genesis
section. Specifics related to the CT modality will be
described here.
3.2.1.2.1 GE CT Advantage Image data
The Image Extract Tool is used in the same way
as on the Signa to extract an image from the
database into a single file, either asis or
using the requested compression and packing
mode. The Genesis file contains headers
consisting of several components in common with
MR and then a specific CT or MR header.
Theroetically, one should be able to use
"/usr/g/insite/bin/ximg -g" to extract a
prototype C header file describing the file
format, as on the Signa, though last time I
tried this on a High Speed Advantage this didn't
work. Some of the more interesting fields in
the CT image header include:
image header - for CT (1020 bytes long):
194 - float - table start Location 198 - float - table end
Location 202 - float - table speed (mm/sec) 206 - float - table
height 224 - float - gantry tilt (degrees)
3.2.1.2.2 GE CT Advantage Archive format
See the GE MR Signa 5.x Archive format.
3.2.1.2.3 GE CT Advantage Raw data
Again, unknown. Please fill in this space.
3.2.1.3 GE CT Pace
References (see the GEMS image format information contacts
section):
- 46-021856 CT Pace Image Data Format -
46-021862 MR Max Image Data Format
The Pace is a CT scanner made by Yokogawa Medical
Systems(YMS) in Japan. The format documents I have for it
are partially in Japanese and partially in English, but
they get the job done. I have only tested the following
on a few images that were extracted off a nine-track tape,
so the offsets to the image header fields may not be
correct in other cases, but here are "eye-catcher" fields
at the start of each header which should be easy to find.
The format seems to be shared with the GE MR Max family.
The images described in the documents have a 512 byte
study header that begins with "!STD" and an image header
of 1024 bytes that begins with "!IMG". In the image that
I had to play with, there was a 256 byte header that I am
not familiar with tacked on the front, presumambly
something to do with being a mag tape rather than a disk
image. Anyway this meant that the offset to the study
header was 256 bytes, the image header was 768 bytes, and
the compressed image data began at 1792 bytes.
I don't know what kind of host is used on the Pace though
I have seen some cryptic references to "DOS-68K" in the
documents. Regardless, the integers are 16 or 32 bit
big-endian. The image data is stored as SIGNED not
unsigned 16 bit values, same as on the Sytec and
presumably all the YMS systems. Most of the useful dates
and times are provided as string values, however there are
some dates and times that are 32 bit binary integers.
Though not specified in the docs it seems that the dates
are days since an epoch of "0 Jan 1980" and the times are
in milliseconds. Floats are 32 bit IEEE format, dfined in
the Pace documentation as follows:
bit 31 sign (s) (0 is +ve)
bits 30-23 exponent (e)
- unsigned integer - e == 0 for denormalized numbers - 0
< e < 255 for normalized numbers - e == 255 for other
reserved operands
bits 22-0 significand (f)
Normalized numbers:
Exponent:
- bias 127 - range 0 < e < 255
Significand:
- interpreted as 1.f - range 1.0 <= f < 2.0
(-1)^s * 2^(e-127) * 1.f
Denormalized numbers:
Exponent:
- e == 0 - bias 126
Significand:
- interpreted as 0.f - range f != 0
(-1)^s * 2^(-126) * 0.f
Signed Infinities:
- e == 255 - f == 0
Not-a-numbers:
- e == 255 - f != 0
The image header has a chunk in the middle where
different values are defined for CT and MR. One can use
the first byte of the model number field to distinuish
the two modalities. Some of the more important study and
image header values are:
Study header (offset 256 bytes, length 512 bytes):
Offset Type Length Meaning Units or values
0x0 string 4 Eyecatcher !STD 0x6 byte 1 Modality 1=CT,2=MR 0xa string 5
Study Number 0x10 datestring Study Date yyyy/mm/dd 0x1a timestring Study
Time hh/mm/ss.xxx 0x26 string 12 Patient ID 0x36 string 12 Patient Name
0x50 string 6 Patient Age yyy;mm 0x5c string 2 PatientSex" 'M ','F '
0xbc string 4 Contrast media 'NO C','+C '
Image header (offset 768 bytes, length 1024 bytes):
Offset Type Length Meaning Units or values
0x0 string 4 Eyecatcher !IMG 0x6 byte 1 Modality 1=CT,2=MR 0xa string 5
Study Number 0x10 string 2 Series Number 0x12 string 2 Acquisition
Number 0x14 string 2 Image Number 0x20 datestring Image Date yyyy/mm/dd
0x2a timestring Image Time hh/mm/ss.xxx 0x40 string 2 'H '=Head First,'F
'=Feet First 0x42 string 2 'SP'=Supine,'PR'=Prone,
'LL'=Left Lateral Decubitus, 'RL'=Right Lateral
Decubitus,'OT'=Other
0x44 string 6 Anatomic location 0x50 string 4 'AX '=Axial,'SAG
'=Sagittal,'COR '=Coronal 0x54 float32 Slice position by body coords HF
mm 0x58 float32 Slice position by body coords AP mm 0x5c float32 Slice
position by body coords LR mm 0x6c string 4 Scan fov cm 0x70 string 4
Scan thickness mm 0xa0 string 4 Contrast media 'NO C','+C '
0x188 float32 Recon center X mm 0x18c float32 Recon center Y mm 0x190
string 4 Recon FOV cm [xx.x] 0x1a0 u_int16 Pixels in X-axis 0x1a2
u_int16 Pixels in Y-axis 0x1a4 float32 Pixel size mm 0x1b0 float32 Mag
center X mm 0x1b4 float32 Mag center Y mm 0x1b8 float32 Mag factor
For CT only:
0xc8 string 5 Gantry tilt machine coords degrees 0xe0 string 5 Exposure
time ms 0xe6 string 3 Tube current mA 0xea string 5 Exposure mAS 0xf0
string 3 KVP 0xf4 string 2 'CW'=Clockwise,'CC'=CounterClockwise
For MR only:
0xc0 string 5 Tilt ordered by user Axis+/-Angle [xx+/-xx] 0x100 string 2
Echo number 0x102 string 2 Number of echoes 0x104 string 2 Slice number
0x106 string 2 Number of slices 0x108 string 2 Number of excitations
0x10a string 5 Repetition time ms 0x110 string 5 Inversion time ms 0x115
string 5 Echo time ms 0x130 string 4 Magnetic flux density (T)
Unlike the Sytec sample images I had, compression was
used in the Pace images I received. This is a neat
scheme that uses both Run Length Encoding and
Differential Pulse Code Modulation. Essentially, each
byte may be a flag value 0x81 which indicates the next
byte is a run length of the current pixel, or a flag
value 0x80 which indicates that the current mode should
be toggled between "reference" mode, in which the
subsequent 16 bit words are new pixel values, or
"difference" mode, in which case subsequent bytes are
signed differences added to the current pixel value. The
initial mode is "reference" mode. Runs do extended
across horizontal line boundaries.
I am not totally clear from the documentation or the
sample images where in the header is the flag to say
compression is in use or not. It is probably bit 5 of
the Image Attribute field in offset 0x1ac in the image
header, where a false value specifies DPCM and a true
value specifies uncompressed or "Original" encoding. The
docs say this is for optical disk only, but the
compressed image from tape I have has this bit false,
which is correct.
The following piece of code will decode such a compressed
image:
static void copypaceimage(istream& instream,ostream& outstream,
Uint16 width,Uint16 height)
{ // NB. the exclusive or with 0x8000 makes the signed Pace values unsigned //
which is what the PGM convention is ... just omit the ^0x8000 // everywhere if
you want the data left signed.
unsigned i; Int16 pixel=0; enum Mode { Difference, Reference } mode =
Reference; for (i=0; i<height*width;) {
unsigned char byte; instream.read(&byte,1); if (!instream)
break; if (byte == 0x80) { // Mode switch
if (mode == Difference)
mode=Reference;
else
mode=Difference;
} else if (byte == 0x81) { // Run length flag
instream.read(&byte,1); if (!instream) break; unsigned
repeat=byte; i+=repeat; while (repeat--)
write16little(outstream,pixel^0x8000);
} else {
if (mode == Difference) {
pixel+=(signed char)byte;
} else {
pixel=byte<<8; instream.read(&byte,1); if
(!instream) break; pixel|=byte;
} write16little(outstream,pixel^0x8000); ++i;
}
} if (!instream) cerr << "Premature EOF byte " << i << "\n" << flush;
}
3.2.1.4 GE CT Sytec
I don't have one of these either, and it turns out that
the format is NOT the same as the Pace as GE Milwaukee
initially thought. The format may be shared with the
Vectra, but this is not known for certain. I do have a
few sample images and have worked out many of the values
in the headers. The format may be available from Yokogawa
in Japan. Milwaukee apparently doesn't have it.
The host is an MS-DOS clone using the J-DOS operating
system, a Japanese version of DOS to handle 16 bit Kanji
characters. Alan Rowberg tells me it has a 5.25" drive
that writes disks that are unreadable by anything else in
the universe.
The images have a header of 3752 bytes and are followed by
16-bit signed integers. The surround is -1500 which is
probably -1500 H.U. The sample files I had did not use
any form of compression.
The data formats are big-endian. Fortuitously the
date/time format is the same as unix ... a 32 bit
unsigned integer containing seconds since an epoch of
00:00:00 GMT 1 Jan 1970. Floats are 32 bit IEEE format as
described in the Pace format.
The head first/feet first and prone/supine fields in the
Sytec file are not known. The sense and identification of
corners in the Sytec sample files was done by guess work,
and may be wrong if the samples weren't scanned head first
supine, and the images are not supposed to be looked at
from bottom up in the usual convention.
The header is 3752 bytes long. The known header values
are (byte offsets from 0):
Offset Type Meaning Units or values
7 string ModelNumber
126 string Organization 204 string PatientID 217 string PatientName
328 datetime ExamDateTime 402 string ExamDescription 425 string Modality
444 string ExamStationID
1164 int16 ExamNumber 1166 int16 SeriesNumber 1172 datetime SeriesDate
1176 string SeriesDescription 1206 string SeriesStationID
1224 int16 ScanType # 1=axial,3=scout 1240 string AnatomicalReference
1280 float32 SeriesStartLocation 1288 float32 SeriesEndLocation
2192 u_int16 ImageExamNumber 2194 u_int16 ImageSeriesNumber 2196 u_int16
ImageNumber 2204 datetime ScanDateTime 2208 float32 ScanDuration #?
secs 2212 float32 SliceThickness # mm 2216 u_int16 XMatrix 2218 u_int16
YMatrix 2220 float32 FieldOfView # mm 2224 float32 ScoutLength # mm 2228
float32 XDimension # mm 2232 float32 YDimension # mm 2236 float32
XPixelSize # mm 2240 float32 YPixelSize # mm
2310 u_int16 ScoutOrientation # 0=none,1=ap,2=lateral 2316 float32
TablePosition # mm 2320 float32 SliceCenterX # mm 2324 float32
SliceCenterY # mm 2328 float32 SliceCenterZ # mm 2332 float32
NormalVectorX # unitized 2336 float32 NormalVectorY # unitized 2340
float32 NormalVectorZ # unitized 2344 float32 TopRightHandCornerX # mm
2348 float32 TopRightHandCornerY # mm 2352 float32 TopRightHandCornerZ #
mm 2356 float32 TopLeftHandCornerX # mm 2360 float32 TopLeftHandCornerY
# mm 2364 float32 TopLeftHandCornerZ # mm 2368 float32
BottomLeftHandCornerX # mm 2372 float32 BottomLeftHandCornerY # mm 2376
float32 BottomLeftHandCornerZ # mm 2384 float32 ScoutStartLocation # mm
2388 float32 ScoutEndLocation # mm 2408 int32 GeneratorVoltage # kVP
2412 int32 TubeCurrent # mA 2416 float32 GantryTilt # degrees
2716 float32 XReconOffset # mm 2720 float32 YReconOffset # mm
3256 int32 BitsPerSample 3264 int32 DefaultWindowWidth 3268 int32
DefaultWindowLevel
3.2.1.5 GE CTI
The GE CTI family of scanners are based on the IOS
platform, but fully
support DICOM both on the network and
on MOD media. hence it is rarely if
ever desirable or necessary to get
involved with the internal format
within the SGI host that runs these
scanners. Having said that, it is
worth pointing out that internally
images may be stored in a Genesis like
format, with the same header layout
except that some fields are 32 bit
rather than 16 bit aligned (like on AW
from which the IOS platform was
derived), or in a true DICOM format,
with a Part 10 style meta-header,
except that the meta-header is encoded
in implicit not explicit little endian
(since it was designed and implemented
before the standard Part 10 was
finished and hence used the convention
of early drafts).
None of this should be of consequence however, since
images should always
be exported from CTI scanners using
network transfer or on DICOM media.
There are a few caveats however, both for the network and
for media.
For network transfers, be absolutely sure that the storage
SCP accepts
only DICOM standard SOP classes during
association negotiation, and is not
promiscuous ("I will store anything of
any SOP class"). Otherwise the CTI
will by preference send proprietary GE
SOP Classes of the ID/NET 2.0 variety,
which are very DICOM like but are
sufficiently different from the
standard CT sop class to cause
problems. The SOP Class UIDs of the
ID/NET 2.0 SOP CLasses are specified
in the conformance statement and if
you absolutely must know what they
contain there is an old service
direction that describes them that is
probably still available.
For the DICOM MOD media, the problems are more serious,
and some of them
are described in the more recent CTI
conformance statement and are further
explained here. Note that all these
problems have been fixed, so that more
recent CTI, MR LX and AW 3X devices
should be writing good conformant
media but still be able to read the
old "bad" media". However since there
may be shelves full of "bad" media one
needs to be aware of the details of
the problem. There is more bad CT
media around than MR and AW since the
fix came later to the CTI.
General details of the encapulsation
and JPEG encoding are defined in DICOM
Part 5 and ISO 10918-1, and explained
in this FAQ in DICOM Compression.
Specific details of the GE bugs are
defined here, as well as being
described in more recent GE CTI
Conformance statements. See for
example section 3.4.2 of GE Direction
2162114-100 High Speed Advantage 4.1
and 5.3 Conformance Statement.
There are two classes of problem, one
related to the DICOM encapsulation,
and the other to the JPEG encoding
itself.
- DICOM encapsulation
- Incorrect byte order of Item
and Sequence Delimiter tags
- JPEG Encoding
- Incorrect Huffman Table
selector (11 not 00) - Incorrect
predictor calculation (inverted)
- Incorrect predictor
initialization at end of row
Even though all DICOM encapsulated transfer syntaxes
specify little endian
byte order for all non-pixel data
values and for all element tags and
value lengths, inadvertantly some of
the delimiter and item tags in GE
encapsulated pixel data are sent in
either big endian for each of the
group and element of the item and
sequence delimited tags, or in little
endian for the concatenated value of
group and element as af they were a 32
bit word. That is instead of
(FFFE,E000) Item being sent as
FE,FF,00,EO as specified in the
standard, it might be seen as
FF,FE,E0,00 or 00,E0,FE,FF. Instead
of (FFFE,E0DD) Sequence Delimiter
being sent as FE,FF,DD,EO, it might be
seen as FF,FE,E0,DD or DD,E0,FE,FF.
Note also that if the Item tag is
encoded wrong, then the VL field is
also incorrectly encoded as a big
endian 32 bit word instead of a little
endian 32 bit word.
In the GE JPEG codec output, the JPEG 'SOS' header defines
the Huffman table selector
codes to find the appropriate Huffman
table. These are incorrectly coded
these as 0x11. They should have been
0x00, since those are the values
assigned in the "DHI" header where the
Huffman tables are actually sent.
This bug manifests itself as a
"Huffman table not found" error from
an unpatached decoder. It also serves
as a useful flag to a patched decoder
that this bug (and others are present)
and allows a single decoder to handle
both good and bad GE compressed bit
streams.
The incorrect GE JPEG computation of the difference to be
Huffman encoded was computed as (Predictor - value) when
it should have been calculated as (value - Predictor).
The result is that the decompression with an unpatched
decoder results in a "negative" of the original image.
Note that GE only uses Selection
Value 1 predication, so there is no
need to patch other predictors.
The predictor value used at the beginning of each line
used the
last value of the previous line in the
image, instead of the first element of
the line above the current line, and
for the first line, the unsigned value
that is half the full scale range for
the "sample precision". This
manifests itself as a wierd "banding"
across the image as predictions get
offset by increasing errors.
An example of code that copes with both the standard and
GE
bugs in JPEG compression can be found
in the patches to the Stanford PVRG
JPEG (see JPEG Sources).
An example of code that copes with both the standard
encapsluation and GE
bugs in encapsulation can be found in
dicom3tools
"libsrc/include/pixeld/unencap.h". A
section of that code (with some of the
error handling removed) is reproduced
here.
size_t read(void)
{
// - non-pixel data is always LE, including fragment
delimiters and lengths // - 1st item is offset table,
may have zero VL // - other items are fragments // -
finally sequence delimitation tag (with zero VL) // -
each delimiter is 2 byte group,2 byte element, 4 byte
VL, little endian // - Item tag is (0xfffe,0xe000) (GE
mistake is 0xfeff,0x00e0 or 0xe000,0xfffe) // - Seq
delimiter is (0xfffe,0xe0dd) (GE mistake is
0xfeff,0xdde0 or 0xe0dd,0xfffe) // - when GE mistake is
present, fragment 32 bit VL is also swapped
length=0;
while (!lefttoreadthisfragment && !finished && !bad) {
Uint16 group=read16(); Uint16 element=read16();
Uint32 vl=read32(); if (group == 0xfffe || group
== 0xfeff || group == 0xe000 || group == 0xe0dd)
{
if (group != 0xfffe) {
cerr <<
"UnencapsulatePixelData::unexpected
group (? bad byte order)=" <<
hex << group << dec << endl;
} if (element == 0xe0dd || element ==
0xdde0 || group == 0xe0dd) { // Sequence
Delimiter Tag
if (element != 0xe0dd) {
cerr <<
"UnencapsulatePixelData::unexpected
element (? bad byte
order)=0x" << hex <<
element << dec << endl;
} Assert(vl == 0);
finished=true;
} else /* if (element == 0xe000) */ { //
Item Tag
bool vlbyteorderwrong=false; if
(element != 0xe000) {
cerr <<
"UnencapsulatePixelData::unexpected
element (? bad byte
order)=0x" << hex <<
element << dec << endl;
vlbyteorderwrong=true;
} if (++fragmentnumber > 0) {
Assert(vl); // Zero
length fragments thought
not to be legal if
(vlbyteorderwrong) {
lefttoreadthisfragment=
(((Uint32)vl&0xff000000)>>24)
+(((Uint32)vl&0x00ff0000)>>8)
+(((Uint32)vl&0x0000ff00)<<8)
+(((Uint32)vl&0x000000ff)<<24);
cerr <<
"UnencapsulatePixelData::assuming
VL also had bad
byte order,
using 0x" << hex
<<
lefttoreadthisfragment
<< dec << endl;
} else {
lefttoreadthisfragment=vl;
}
} else {
// skip the offset table
Assert(vl%4 == 0);
unsigned i=0; while (vl)
{
Uint32
offset=read32();
vl-=4; ++i;
}
}
}
} else {
// bad tag group in encapsulated data
bad=true;
}
}
if (lefttoreadthisfragment && !bad) {
length=unsigned(lefttoreadthisfragment >
maxlength ? maxlength :
lefttoreadthisfragment); if
(istr->read(buffer,length)) {
length=istr->gcount();
} else {
bad=true; length=0;
} lefttoreadthisfragment-=length;
}
return length;
}
3.2.2 Siemens CT
Some general comments about the way in which Siemens image
headers, and the concept of native file formats and exported SPI
formats are to be found in the section on Siemens MR.
3.2.1.1 Siemens Somatom DR
- NOT in SPI format - fixed format - files 133120 bytes
(for 256 square images) - image pixel data 256*256*2
little endian - image pixel offset 2048 bytes - same for
axial images and topograms (scouts)
This description pertains to the DR family, and possibly
also earlier Siemens CT models, but I have no files from
these to test.
The files are in fixed format (cf. the early Magnetom
format which is similar, but has block pointers) with
three major blocks of entries:
- binary data - offset 0 - 512 bytes - text overlay - offset 512 - 960
bytes plus 676 bytes free - image pixel data - offset 2048 - 131072
bytes
The binary data block is filled with the usual cryptic
enumerated values and useful parameters. Some of the more
interesting ones are:
- binary data block:
66 - byte - archive mode (0=raw data,B=256,C=512) 67 - byte -
archive mode (0=uncompressed,
2=compressed)
72 - short - matrix size (256 or 512)
130 - byte - scan mode (P=image data,R=raw data) 131 - byte -
scan mode (0=tomogram,Q=quick,S=serial,
C=cardiac,T=topogram,X=test,H=chronogram)
132 - short - fov - mm 134 - short - scan time - secs * 10 136 -
short - kv 138 - short - dose - maS 140 - short - slice
thickness - mm 142 - short - gantry tilt - degrees 144 - short -
table position - mm 146 - short - table height - mm 148 - short
- scan mode (1=standard(360),
2=quickscan(240),4=topogram)
236 - short - view direction (1=cranial,-1=caudal) 238 - byte -
head position (0=head first,
1=feet first)
239 - byte - patient position (0=supine,
1=prone,2=r lat dec,3=l lat dec)
310 - short - window width A 312 - short - window center A 314 -
short - window width B 316 - short - window center B
Unfortunately, the patient identification information is
NOT stored in the binary data block, rather one has to
extract it from the image text overlay block, which
consists of 960 characters (24 lines of 40 characters
WITHOUT carriage control characters) in a fixed format.
This is where what you see overlayed on the filmed images
is stored. Some of these values are duplicates of what is
in the binary data block, but things like the patient name
and so on are here and nowhere else :(
0123456789012345678901234567890123456789
0 SOMATOM DR2 ST. ELSEWHERE GEN HOSP 40 999999-9999 JOHN DOE
EF2 80 01-JAN-90 FRONT 35B 120 13:31:22 H/SP 160 200 SCAN 60 L
240 E 280 F 320 T 360 400 440 480 520 560 600 640 680 720 TI 5
760 KV 125 800 AS .35 840 SL 2 880 GT 0 920 TP 144
- text overlay block: (some of this is guess work)
0 - char[14] - product 15 - char[25] - hospital name 40 -
char[12] - patient number 53 - char[22] - patient name 80 -
char[2] - date - dd 83 - char[3] - date - mmm 87 - char[2] -
date - yy 120 - char[2] - time - hh 123 - char[2] - time - mm
126 - char[2] - time - ss 156 - char[1] - H=head first,F=feet
first 158 - char[2] - SP=supine,PR=prone,
RP=right lateral decubitus, LP=left lateral
decubitus
205 - char[4] - slice number 723 - char[4] - scan time - secs
763 - char[4] - kv 803 - char[4] - dose - AmpS 843 - char[4] -
slice thickness - mm 883 - char[4] - gantry tilt - degrees 923 -
char[4] - table position - mm
If anyone knows what "EF2" and "35B" stand for I would
love to know - I presume they are something like the
filter used, or field of view or something ?
Also the DR family don't seem to be aware of the concept
of a hierarchy of examination/study and series numbering,
which makes it annoying to try to import them into PACS
systems :( Correct me if I am wrong but they just seem to
keep bumping up the slice number for each patient as each
group of scans is done.
3.2.2.2 Siemens Somatom Plus
There seem to be different formats for different versions
of the machine. Either that or some sites have PACS
software and some don't or something. Anyway, one set of
files that were sent to me used a fixed format header much
like the DR family, but of different length and with
different fields. I have not yet adequately deciphered
this header but will include it here when I have. This
may be what is referred to as the "original header" stored
in the SPI format.
Another site uses a Siemens version of SPI, containing the
following private data elements. Note that there is
overlayed data in the high four bytes of the image pixel
data, and that there seems to be a bunch of padding in the
middle. The intent seems to be to store the "original
header" and the image pixel data at accessible, presumably
standard locations, presumably indexed by the byte offsets
and lengths described in group 9. This is a shame because
it seems that none of the really interesting CT attributes
have been included in the SPI form, although SPI private
tags are available for lots of CT parameters. I don't
have one of these image to test this theory, someone just
sent me an output of the attribute dump.
SPI private tags:
(0009,0010) <SPI RELEASE 1> (0009,0011) <SIEMENS MED> (0009,1011) SPI RELEASE 1
UID <049S03CT031995011712072452> (0009,1040) SPI RELEASE 1 DataObjectSubtype
[0x0000] (0009,1041) SPI RELEASE 1 DataObjectSubtype <IMA TOPO> (0009,1110)
SIEMENS MED RecognitionCode <CT 1.4> (0009,1130) SIEMENS MED
ByteOffsetOfOriginalHeader (0009,1131) SIEMENS MED LengthOfOriginalHeader
(0009,1140) SIEMENS MED ByteOffsetOfPixelmatrix (0009,1141) SIEMENS MED
LengthOfPixelmatrixInBytes
(0011,0010) <SPI RELEASE 1>
(0021,0010) <SIEMENS MED> (0021,1010) SIEMENS MED Zoom <01.0> (0021,1011)
SIEMENS MED Target <000.000\00.000> (0021,1012) SIEMENS MED TubeAngle <0270>
(0021,1020) SIEMENS MED ROIMask [0xf000]
Overlay descriptions (overlays already in image pixel data):
(6000,0040) ROI <G> (6000,0102) BitPosition [0x000c] (6000,0102) OverlayLocation
[0x7fe0]
(6002,0040) ROI <G> (6002,0102) BitPosition [0x000d] (6002,0102) OverlayLocation
[0x7fe0]
(6004,0040) ROI <G> (6004,0102) BitPosition [0x000e] (6004,0102) OverlayLocation
[0x7fe0]
(6006,0040) ROI <G> (6006,0102) BitPosition [0x000f] (6006,0102) OverlayLocation
[0x7fe0]
More SPI private stuff ... padding and original header ...
(7001,0010) <SIEMENS MED> (7001,1010) SIEMENS MED Dummy
(7003,0010) <SIEMENS MED> (7003,1010) SIEMENS MED Header
(7005,0010) <SIEMENS MED> (7005,1010) SIEMENS MED Dummy
3.2.2.3 Siemens Somatom AR
Unknown.
3.2.3 Philips CT - Big black hole
3.2.4 Picker CT
Grey hole perhaps. This information probably pertains to the IQ
and PQ CT models, though I have no sample images to experiment
with yet. I am told that:
- axial images are 512x512 - pilot images are 1024x1024 -
uncompressed images are 12 bits stored in 16 bits - don't know how
to handle compression scheme - raster order is as usual, by row,
TLHC first - 8k header to be skipped
3.2.5 Toshiba CT - another black hole 3.2.6 Hitachi CT - another black
hole 3.2.7 Shimadzu CT - another black hole 3.2.8 Elscint CT - another
black hole
3.2.9 Imatron CT
The following information is included verbatim from that kindly
supplied by Cameron Ritchie:
Imatron File Format
In this document, the Imatron file format is described. Imatron makes no
guarantees that future Imatron files will be compatible with the attached
format. This format is current as of 2/29/96.
The format described here is generally true for files produced by all Imatron
scanners (C-100, C-150L, C-150, C-150XP, C-150LXP); however, some small
differences may be found. The file format described below is valid for image
files on the scanner's RT-11 disks. What is not described is how to actually
get one of these files off the RT-11 and on to a workstation or PC for
conversion. This procedure is actually almost more difficult than the
conversion! There are three options for getting files off the scanner; only one
does not require additional hardware. The options are as follows:
- Use the RT-11 program "XFR" to transfer the image
file from the RT-11 to the VxWorks based VME computer. XFR can be run from
the RT-11 dot prompt. Following an XFR transfer (provided that the VME
computer is on a network), one can ftp to the VME computer and transfer the
file to some other computer. One may or may not need to swap the bytes in
the file after the ftp transfer. The actual procedure for using XFR is
relatively complicated, and we recommend that the interested researcher talk
to his or her field service engineer to get all the details.
- Use the PC-program "UPOW". The use of this program
requires that GPIB interface cards be installed in both the PC and in the
scanner console. Interested researchers should contact Imatron about how to
obtain the UPOW software and hardware.
- Use the shared memory interface "MEGALINK". The
use of this program requires that shared memory interface boards be
installed in the VME computer and in a compatible workstation. Compatible
workstations can be purchased from Siemens, ISG Technologies, or Cemax.
Two demo image extractors are available for download. Both are available with
source code, and Imatron does not guarantee either program's accuracy. The
first program converts Imatron format files to headerless files. The
second program
converts Imatron files to Siemens Somatom, headerless, DICOM, or TIFF. Command
line help can be obtained for either program by typing program_name -h.
Imatron hopes that the information contained here is useful to the research
community. Assistance, within reason, can be obtained by contacting:
Cameron J. Ritchie, Ph.D. Applications Scientist Imatron Inc. 389 Oyster
Point Blvd. South San Francisco, CA 94080 E-mail: cameron...@imatron.com
Disk Data-File Formats
Scan data collected are stored as raw data in files on the VME disk drive.
After reconstruction they are stored as image data files on the RT-11 disks.
These files comprise header information and the acquired data. An Imatron file
is a set of information about multiple slices. Each file contains:
-A Control Block -A Single File Header -A Slice-Header Position Table, and -One
Slice Header (for each slice in the file).
Block 0: Control Block
The control block is the first block of an Imatron file and contains information
necessary for interpreting the rest of the file (Table 2-1).
Table 2-1: Words in a Control Block
WORD DESCRIPTION
0 Pointer to first block in the file header
1 Number of entries in the file header
2 Pointer to first block of the file header data
3 Pointer to first block in the slice header
4 Number of entries in the slice header
5 Pointer to first block of the slice header position
table
6 Number of words in a header table entry
7 File type version number
8 Number of blocks of detector offset data
9 Number of blocks in file header table
10 Number of blocks of file header data
11 Number of blocks in slice header
12 Number of blocks in slice header position table
13 Number of blocks for each section of slice header
data
14 Pointer to start of detector offset blocks
15-255 0
--->
File and Slice Headers
Imatron file and slice headers store information about: file organization, the
patient, scanning, reconstruction, and how to perform image analysis on the
data. Information in these headers is not stored in fixed locations in the
file. Instead, there is a symbol table that references the header values by
name.
There are two symbol tables in each file: the file-header symbol
table (referred to as the file header or file-header table), containing names
and pointers into a single file-header data area; and the slice-header symbol
table (referred to as the slice header or slice-header table), which uses the
same format but its pointers are used for all the slice-header data areas (one
per slice).
The file header and the slice header are composed of pointer/descriptor units
which point to variables in the data blocks. Each unit is 6 words (12 bytes)
long and organized as shown in Table 2-2.
Table 2-2: Unit Organization
BYTE Contents
1-6 ASCII variable name, padded with null bytes
7 Null byte (0)
8 ASCII variable type (I => Integer, B => Byte, F =>
Floating Pt.)
9-10 Integer pointer to the word number in the block where
the data for this variable starts
11-12 Number of data values of the type described in byte 8.
The integers contained in bytes 9-10 and 11-12 are stored with the least
significant byte in the first byte, and the most significant byte in the second
byte.
The following is an example of how the file-header parameter ICMNTS is defined:
BYTE: 1-6 7 8 9 10 11 12
ICMNTS 0 'B' 37 0 80 0
Parameter variables:
-name is ICMNTS (bytes 1-6) -and is a byte variable (byte 8) -and starts at word
number 37 in the block (bytes 9,10) -and contains 80 bytes of data (bytes
11,12).
One block can contain up to 42 pointer/descriptor units.
Slice-Header Position Table
The slice-header position table contains a list of unsigned integer pointers to
the various slice-header data blocks. The first word of this table points to
slice-header data block 1, the second to slice-header data block 2, etc.
ECG Data
ECG data is stored in the raw (.VME) and image files for ECG-triggered studies.
The file header variable ITRTYP, points to the starting block in the file for
this set of data, which, if present, is 32 blocks long. There is no slice
header associated with the data.
File header parameters are shown in Table 2-3; slice headers are shown in Table
2-4.
Image Data-File Formats
The C-150 scanner produces axial slices by sweeping an electron beam along one
of four target rings (Target A, B, C, or D). X-rays produced by the scanning
electron beam are detected by a pair of solid-state detector rings (Detector
Rings 1 and 2).
In an N-image (Imatron image) file there are N slices, 1 slice per image. The
slice-header parameters, NROWS and NCOLS, define the number of rows and columns
in the stored rectangular image.
Data is not compressed. The first NCOLS words in the
slice are the first row, the second NCOLS words are the second row, etc. Image
data are converted to Hounsfield units by subtracting 1000 (decimal) from each
word. The resulting numbers range from -1000 to +3095 inclusive (Imagraph).
Table 2-3: Data File Header Format
INDEX NWDS NAME DESCRIPTION
1 1 IFHLEN The number of 256 word blocks in the
file header.
2 1 ISHLEN The number of 256 word blocks in the
slice header.
3 5 IAFN The ASCII file descriptor. (6 char.
name,'.',3 char. extension)
8 5 IADATE ASCII date string. (9 character
string right-padded with a blank.
13 4 IATIME ASCII time string. (8 character
string)
17 6 IPATID ASCII patient ID number. (12 chars.)
23 15 IPATNA ASCII patient name. (30 chars.)
38 40 ICMNTS ASCII comments. (80 chars.)
78 1 NDETS The number of detectors. (432 or
864)
79 63 IDEMAP The detector status map for the
file. All bits defined as 1=working,
0=inoperative. Channel k's status is indicated in
word IW=1+(k-1)/16, [integer arith.] of IDEMAP, by
bit
IBIT = k - (IW-1)*16 - 1.
142 1 ISTOB The starting block for detector
offset measurements. (0 for no offsets recorded.)
143 1 NSLICE The number of slices in the file.
144 1 IORGAN The file organization code:
-2 = unsorted raw MM data (AIR, PIN or OFFSET) -1
= unsorted raw MM data (Non-calibration) 0 =
source-fan data 1 = detector-fan data 2 = image
(rectangular) data 3 = tuning point data 4 =
deflection buffer data 5 = processed calibration
data 6 = processed AIR data 7 = processed OFFSET
data
145 1 ITTICK The DAS clock period is
microseconds.
146 1 NPHVEW The number of phantoms.
147 1 IDATYP 0 = DAS output words (All RAW data)
1 = Integer 2 = Floating point (Sinogram,
tuning,offsets) 3 = Scaled 11-bit integer data
(image & screen save) 4 = AP400 block floating
point mantissas 5 = MM address data (calibration
data) 6 = Octal data (deflection buffer files) 7 =
Packed Fast Raw Averaged Data 8 = Scaled 12-bit
integer data (image & screen save)
148 1 NDETOM No. of detector offset measurements
149 2 XMMTMU The scale factor to change from mm
to MIP machine units (units are m.u./mm)
151 1 IREP The no. of DAS samples per detector
per source fan. IREP = 3 for a 50ms scan, IREP =
6 for a 100ms scan.
152 2 PIXLEN Length in mm. of a pixel, from
reconstruction
154 1 NLEVEL Number of levels in the file
155 1 NPLEVL Number of images per level (valid in
raw image files. Level number is an integer from
1 to NLEVEL. Closest to the gun is first.)
156 1 IREF 2 Byte ASCII description of the
reference pt.
157 1 ISTUDY Study type:
-199 to -100 reserved for test & calibration
"studys" (Not Reconstructable!) -1 =
SCREEN SAVE => No analysis possible. 0 = SPECIAL
STUDY => Anything not covered below. Atypical
study 1 = LOCALIZATION => single scans, 2 images
per scan, N scans at arbitrary levels (in pairs)
(50 ms) 2 = FLOW STUDY => Typically, a set of
scans triggered periodically. 3 = MOVIE STUDY =>
Typically, many scans taken continuously. 4 =
AVERAGE VOLUME=> Averaged data from a volume study
on a single target ring 5 = VOLUME STUDY =>
various times at lots of levels (table motion) 6 =
AVERAGE FLOW => Averaged data from a flow study on
a single target ring 7 = CONTINUOUS VOLUME (CVS)
51 = IMAGE AVERAGING 52 = REFORMAT 53 to 61
reserved for FUNCTIONAL IMAGE PROC. 53 = FIP
Maximum Difference 54 = FIP Time to Peak 55 = FIP
Area Under the Curve 56 = FIP Center of Mass 102 =
IMAGE SUBTRACTION FLOW 103 = IMAGE SUBTRACTION
MOVIE 105 = IMAGE SUBTRACTION VOLUME 106 = IMAGE
SUBTRACTION AVERAGE FLOW
158 10 ICONTR Type of contrast (20 characters)
168 2 DOSECN Contrast dose in cc
170 10 INJSIT Injection Site (20 characters)
180 10 ISTRES Type of stress (20 characters)
190 7 IRPHYS Referring physician's last name (14
chars)
197 7 IRADIO Radiologist's last name (14 chars)
204 2 ITECH Radiation technologist's initials (3
chars)
206 5 IBDATE Patient's birthdate (9 chars (ex.
07-jan-17))
211 1 ISTHCK Slice thickness, mm.
212 1 ICALIB Calibration number
213 1 KERNEL Desired kernel flag
214 1 ITRTYP trigger type:
1 = manual 2 = timed 3 = ecg with no extra data
else it's a pointer to ecg data in the file
215 1 IPATSZ patient size:
1 = small 2 = medium 3 = large 4 = shoulder/pelvis
kluge
216 1 IPRLVL regular reconstruction's first level
to recon:0 = none else 1 to nlevel
217 20 IDIAG diagnosis comment
237 9 IHOSP hospital (actually scanner)
246 4 BOLTIM Bolus times
250 1 NSPLIT Number of images to be created from
each raw slice
251 1 IDLINP Delete raw data flag:
0 = do NOT delete after recon 1 = delete after
complete recon
252 2 CDENS Density of contrast
254 1 IOFMIN Time since midnight in minutes of
last offsets
255 1 IOFDAT Day since dec 31 of last offsets
256 1 NRINGS Number of detector rings used.
257 1 NTARGT Number of targets used.
258 1 ICNREC 0 = not suitable for cone beam
algorithm. 1 = suitable for cone beam algorithm.
2 = suitable and cone beam alg used.
259 6 KERNAM ASCII kernel name used.
260 1 ISNTYP Sinogram type.
261 1 IANTYP Analysis type for ASA
1 = Cone analysis 2 = Air analysis 3 = Pin
analysis
262 1 ISTHCF Slice thickness. LSB = 1/100 mm.
263 1 ICOLL Collimator setting (1=1.5mm, 3, 6)
Table 2-4: Data Slice Header Format
INDEX NWDS NAME DESCRIPTION
1 1 ISDATP Pointer to data for this slice
(Always here!)
2 2 R1MU Linear attenuation co-efficient for
water at this energy and current, ring 1.
4 1 IROTA = 1 clockwise scan,
or = -1 for counter-clockwise scan.
5 2 HVDES Desired high voltage for this scan,
in kV.
7 2 HVACT Actual high voltage for this scan,
in kV
9 1 ICURNT Actual electron beam current, in
milliamps.
10 2 FVDES Desired filament voltage, in volts.
12 2 FVACT Actual filament voltage, in volts.
14 2 FCACT Actual filament current, in
milliamps.
16 1 IRING The detector ring used:
0 = Raw slice with both RINGs interleaved 1 =
RING 1 (closest to gun) 2 = RING 2 (farther from
gun)
17 1 ITARGT The target ring used.
18 1 NSLAVG The number of scans averaged to
produce this slice.
19 2 PICRAD Floating point picture radius in
mm.
21 2 XORG Floating point X coordinate of
reconstruction center (0.0 is isocenter) in mm.
23 2 YORG Floating point Y coordinate of
reconstruction center (0.0 is isocenter) in mm.
25 2 ZOOM Floating point zoom factor (1.0 =
no zoom) for reconstruction
27 1 NROWS The number of rows in the
reconstructed image.
28 1 NCOLS The number of cols in the
reconstructed image.
29 2 VALMAX Maximum value in the slice (in
floating point)
31 2 VALMIN Minimum value in the slice (in
floating point)
33 2 RSCALE Data has been scaled and biased
such that
35 2 RMIN actual data = data/RSCALE + RMIN
37 1 IPATH Holding path flag:
0 = path was HOLDING PATH 1 = path was the first
for that pulse 2 = the slice was NOT the first of
that pulse (slices 2-N for a movie or volume)
38 2 ELAPSE Time, in seconds, since the first
scan
40 1 LEVELN The level number for a given slice
41 2 ISTAGE Old:2 word array, 2nd word unused,
1st word is >=0 if data is present and useful.
43 1 INOUT In-out table pos. relative to ref.
(-0.1 mm)
44 1 IHITE Up-down table pos. relative to
reference (mm)
45 1 ITILT Table tilt relative to horizontal
(degrees)
46 1 ISLEW Table slew relative to straight
(degrees)
47 1 ICPHAS Cardiac phase in % R-R-wave
interval
48 1 IBEAT Heart beat # for this image
49 2 HRATE Heart rate in beats per minute
51 1 IPATOR Integer code for patient
orientation: 0 = not applicable or special case 5
= prone head first flipped + 1 = supine
+ 2 = prone + 3 = decubitus right + 4 =
decubitus left -5 = supine ff (flipped to match
1)
-6 = prone ff (ditto 2) -7 = decub right (ditto
3) -8 = decub left (ditto 4)
Positive refers to HEAD FIRST (head closest to
gun). Negative refers to FEET FIRST.
52 2 SLSIZE Size of slice in words
54 1 ITN Order of Chebychev polynomial
applied to data (only if valid during
calibration, for normal recon ITN = 0).
55 2 R2MU Linear attenuation coefficient for
water at this energy and current, ring 2.
57 1 IVMFLAG Contains bit-map of flags used by
recon.
58 1 NTARGS Number of target sections of this
target ring.
Scanner Operating Modes
The scanner operates in two different modes: Single-Slice Mode (SSM) and
Multi-Slice Mode (MSM).
Single-Slice Mode:
The FILE HEADER variable "IREP" defines Single-Slice
Mode:
IREP = 6 for SSM
The total number of images in the file is the FILE HEADER variable
NSLICE.
The total number of axial slice positions in the file is the
FILE HEADER variable NLEVEL.
In SSM, only Target Ring C and Detector Ring 2 are used.
Each sweep of the beam along Target Ring C takes 100 milliseconds.
The exposure time (in seconds) is determined by the SLICE HEADER
variable "NSLAVG":
Exposure time (seconds) = NSLAVG * 0.1
The axial position for each slice is determined by the SLICE
HEADER variable "INOUT" (which is in tenth mm units):
Slice position relative to reference (in mm) = INOUT/10
Multi-Slice Mode:
The FILE HEADER variable "IREP" defines Multi-Slice
Mode:
IREP = 3 for MSM
The total number of images in the file is the FILE HEADER variable
NSLICE.
The total number of axial slice positions in the file is the
FILE HEADER variable NLEVEL.
In MSM Mode, each sweep of the electron beam along a single
target ring produces a pair of simultaneously acquired, side-by-side axial
slices (1 from each detector ring).
Any combination of target rings (A, B, C, or D) may be used.
Each sweep of the beam along any single target ring takes 50
milliseconds.
The exposure time (in seconds) is determined by the SLICE HEADER
variable "NSLAVG":
Exposure time (seconds) = NSLAVG * 0.05
The axial position for each slice is determined by the SLICE
HEADER variables "INOUT," "ITARGET," and "IRING"
and may be calculated as follows:
KTARGT = ITARGT - 64 /* Convert ascii target to integer */
TAROFF = -20.0 + (4 - KTARGT)*20.0 /* Distance from C to target */
DETOFF = mod(IRING,2)*8 /* Distance from detector Ring 2 to detector */
Slice position relative to reference (in mm) = INOUT/10. + TAROFF + DETOFF
Study Types
The six Imatron study types are described as follows:
SSM Flow (IREP = 6, ISTUDY = 6)
Description: For an N-slice SSM Flow Study, the following
is repeated NSLICE times: A 100-ms sweep of the beam is
performed NSLAVG times along ring C (with 16 ms between
sweeps), and the data for the NSLAVG sweeps are summed
together to produce a single image. All of the data are
acquired at a single axial slice position, sequentially in
time.
File Organization: Slice 1 in the file is the first "time,"
slice 2 is the second "time," ...slice n is the
nth "time."
SSM Cine (IREP = 6, ISTUDY = 3)
Description: For an N-slice SSM Cine study, NSLICE 100-ms
sweeps of the beam are performed along Target Ring C (with
16 ms between sweeps). Each sweep of the beam produces a
single image. All of the data are acquired at a single
axial slice position, sequentially in time.
File Organization: Slice 1 in the file is the first "time,"
slice 2 is the second "time," ... slice n is the
nth "time."
SSM Volume (IREP = 6, ISTUDY = 5)
Description: In an N-slice volume study, the following
sequence is repeated NSLICE times in succession: A 100 ms
sweep of the beam is performed NSLAVG times along ring C
(with 16-ms between sweeps), and the data for the NSLAVG
sweeps are summed together to produce a single image. Then
the patient table moves to a new axial position.
File Organization: Slice 1 in the file is the first "level,"
slice 2 is the second "level," ... slice n is
the nth "level."
MSM Volume (IREP = 3, ISTUDY = 5)
Description: MSM Volume Studies always use Target Ring C
(only), and both Detector Rings 1 and 2. In an MSM VOLUME
STUDY, the following sequence is repeated NLEVEL/2 times in
succession: A 50-ms sweep of the beam is performed NSLAVG
times along ring C (with 8-ms between sweeps) and the data
for the NSLAVG sweeps are summed together to produce a pair
of side-by-side images acquired at adjacent axial
positions. Then the patient table moves to a new axial
position.
File Organization: Slice 1 in the file is the first "level,"
slice 2 is the second "level," ...slice n is the
nth "level."
MSM Flow (IREP = 3, ISTUDY = 1 or 2)
Description: Refer to the general Multi-Slice Mode
description, above. In an MSM Flow study, the following
applies:
N_T = The number of times = NSLICE/NLEVEL
The following action is repeated N_T times:
For a 2-level MSM Flow, the beam sweeps
once on a single target ring (A, B, C, or D) to produce a
pair of side-by-side images acquired at the same
"time."
For a 4-level MSM Flow, the beam sweeps
once on one target ring, then 8 ms later, sweeps on a
second target ring; this produces 4 side-by-side images
acquired at the same "time."
For a 6-level MSM Flow, the beam sweeps
once on one target ring, then 8 ms later, sweeps on a
second target ring; followed 8 ms later by another sweep,
on a third target ring; this produces 6, side-by-side
images acquired at the same "time."
For an 8-level MSM Flow, the beam sweeps once on one target
ring, then 8 ms later, sweeps on a second target ring;
followed 8 ms later by another sweep on a third target
ring, and again, 8 ms later on the fourth target ring; this
produces 8, side-by-side images acquired at the same
"time" (Table 2-5).
Table 2-5: File Organization for MSM Flow
Slice in File Time Axial Position
Index
1 1 use MSM Template info => axial
index i
2 1 use MSM Template info => axial
index ii
3 1 use MSM Templace info => axial
index iii
. . .
. . .
. . .
NLEVEL 1 use MSM Template info => index
nlevel
NLEVEL+1 2 axial index i
NLEVEL+2 2 axial index ii
. . .
. . .
. . .
2*NLEVEL 2 axial index nlevel
2*NLEVEL+1 3 axial index i
. . .
. . .
. . .
(N_T-1)*NLEVEL+1 N_T axial index i
(N_T-1)*NLEVEL+2 N_T axial index ii
. . .
. . .
. . .
N_T*NLEVEL N_T axial index nlevel
MSM Cine (IREP = 3, ISTUDY = 3)
Description Refer to the general MSM description above.
In an MSM Cine study, the following applies:
N_T = The number of times = NSLICE/NLEVEL
NTARGS = The number of targets used = NLEVEL/2
The following action is repeated NTARGS times (once for each target):
N_T 50-ms sweeps of the beam are performed, with 8-ms between
sweeps, along a single target ring (A, B, C, or D); this produces a pair of
images acquired at adjacent axial positions. (See Table 9, below.)
Table 2-6: File Organization for MSM Cine
Slice in File Time Axial Position
Index
1 1 use MSM Template info => axial index
i
2 1 use MSM Template info => axial index
ii
3 2 axial index i
4 2 axial index ii
5 3 axial index i
6 3 axial index ii
. . .
. . .
2*N_T-1 N_T axial index i
2*N_T N_T axial index ii
2*N_T+1 1 use MSM Template info => axial index
iii
2*N_T+2 1 use MSM Template info => axial index
iv
2*N_T+3 2 axial index iii
2*N_T+4 2 axial index iv
. . .
. . .
4*N_T-1 N_T axial index iii
4*N_T N_T axial index iv
. . .
. . .
(NLEVEL-2)*N_T+1 1 use MSM Template info => axial index
nlevel-1
(NLEVEL-2)*N_T+2 1 use MSM Template info => axial index
nlevel
(NLEVEL-2)*N_T+3 2 axial index nlevel-1
(NLEVEL-2)*N_T+4 2 axial index nlevel
. . .
. . .
NLEVEL*N_T-1 N_T axial index nlevel-1
NLEVEL*N_T N_T axial index nlevel
The next part is part4 - proprietary MR formats.