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Medical Image Format FAQ, Part 1/8

( Part1 - Part2 - Part3 - Part4 - Part5 - Part6 - Part7 - Part8 )
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Archive-name: medical-image-faq/part1
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Last-modified: Sun Dec 21 09:16:25 EST 2003
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    part1    - contains index, general information & standard formats
    part2    - contains standard formats (continued)
    part3    - contains information about proprietary CT formats
    part4    - contains information about proprietary MR formats
    part5    - contains information about proprietary other formats
    part6    - contains information about hosts & compression
    part7    - contains general information sources
    part8    - contains DICOM information sources

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or reply to this article. All unknown formats and test images gratefully

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The next part is table of contents.

Subject: Contents

1.  Introduction

    1.1 Objective 1.2 Types of Formats 1.3 In Desperation - Quick & Dirty Tricks

2.  Standard Formats

    2.1 ACR/NEMA 1.0 and 2.0 2.2 DICOM 3.0

	2.2.1 Localizer lines on DICOM images

    2.3 Papyrus 2.4 Interfile V3.3 2.5 Qsh 2.6 DEFF

3.  Proprietary Formats

    3.1 Proprietary Formats - General Information

	3.1.1 SPI (Standard Product Interconnect) 3.1.2 Siemens - Features
	common to multiple families Siemens Vax/VMS Siemens Sparc SunOS Starting up Getting a console Native images Exporting images Physical connection Archive devices Becoming root Reset

    3.2 CT - Proprietary Formats

	3.2.1 General Electric CT GE CT 9800 GE CT 9800 Image data GE CT 9800 Tape
		      format GE CT 9800 Raw data MR GE CT Advantage - Genesis GE CT Advantage Image data GE CT
		      Advantage Archive format GE CT Advantage Raw
		      data GE CT Pace GE CT Sytec GE CTI

	3.2.2 Siemens CT Siemens Somatom DR Siemens Somatom Plus
	      Siemens Somatom AR

	3.2.3 Philips CT 3.2.4 Picker CT 3.2.5 Toshiba CT 3.2.6 Hitachi CT 3.2.7
	Shimadzu CT 3.2.8 Elscint CT 3.2.8 Imatron CT

    3.3 MR - Proprietary Formats

	3.3.1 General Electric MR GE MR Signa 3.x,4.x GE MR Signa 3.x,4.x Image data GE MR
		      Signa 3.x,4.x Tape format GE MR Signa 3.x,4.x
		      Raw data GE MR Signa 5.x - Genesis GE MR Signa 5.x Image data GE MR Signa
		      5.x Archive format GE MR Signa 5.x Raw data GE MR Max GE MR Vectra

	3.3.2 Siemens MR Siemens Magnetom GBS/GBS II Siemens Magnetom GBS/GBS II Native Format Siemens Magnetom GBS/GBS II SPI Format Siemens Magnetom SP Siemens Magnetom SP Native Format
		      Siemens Magnetom SP SPI Format Siemens Magnetom Impact Siemens Magnetom Impact Native Format
		      Siemens Magnetom Impact SPI Format Siemens Magnetom Vision Siemens Magnetom Vision Native Format
		      Siemens Magnetom Vision SPI Format

	3.3.3 Philips MR Philips Gyroscan S5 Philips Gyroscan ACS
	      Philips Gyroscan T5 Philips Gyroscan NT5 & NT15

	3.3.4 Picker MR 3.3.5 Toshiba MR 3.3.6 Hitachi MR 3.3.7 Shimadzu MR
	3.3.8 Elscint MR

    3.4 Proprietary Workstations

	3.4.1 ISG Workstations Gyroview

	3.4.2 GE Workstations GE Advantage Windows

    3.5 Other Proprietary Formats

	3.5.1 Analyze From Mayo

4.  Host Machines

    4.1 Data General

	4.1.1 Data General Data Data General Integers Data General Floating Point

	4.1.2 Data General Operating System Data General RDOS Data General AOS/VS

	4.1.3 Data General Network

    4.2 Vax

	4.2.1 Vax Data Vax Integers Vax Floating Point Vax

	4.2.2 Vax Operating System Vax VMS ULTRIX OSF

    4.3 Sun - Sun3 68000 and Sun4 Sparc

	4.3.1 Sun Data Sun Integers Sun Floating Point Sun

	4.3.2 Sun Operating System

5.  Compression Schemes

    5.1 Reversible Compression 5.2 Irreversible Compression

	5.2.1 Perimeter Encoding

    5.3 DICOM Compression

6.  Getting Connected

    6.1 Tapes 6.2 Ethernet 6.3 Serial Ports

7.  Sources of Information

    7.1 Contacts and Sites 7.2 Relevant FAQ's 7.3 Mailservers 7.4 References 7.5
    Organizations and Societies 7.6 Usenet Newsgroups 7.7 DICOM Information

8.  Acknowledgements

The next part is part1 - general information & standard formats.

1.  Introduction

    1.1 Objective

	The goal of this FAQ is to facilitate access to medical images stored on
	digital imaging modalities such as CT and MR scanners, and their
	accompanying descriptive information.  The document is designed
	particularly for those who do not have access to the necessary
	proprietary tools or descriptions, particularly in those moments when
	inspiration strikes and one just can't wait for the local sales person
	to track down the necessary authority and go through the cycle of
	correspondence necessary to get a non-disclosure agreement in place, by
	which time interest in the project has usually faded, and another great
	research opportunity has passed!  It may also be helpful for those keen
	to experiment with home-grown PACS-like systems using their existing
	equipment, and also for those who still have equipment that is still
	useful but so old even the host computer vendor doesn't support it any

	There is of course no substitute for the genuine tools or descriptions
	from the equipment vendors themselves, and pointers to helpful
	individuals in various organizations, as well as names and catalog
	numbers of various useful documents, are included here where known.

	In addition there are several small companies that specialize in such
	connectivity problems that have a good reputation and are well known.
	Contact information is provided for them, though I personally have no
	experience with their products and am not endorsing them.

	Finally, great care has been taken not to include any information that
	has been released under non-disclosure agreements.  What is included
	here is the result of either information freely released by vendors,
	handy hints from others working in the field, or in many cases close
	scrutiny of hex dumps and experimentation with scanner parameters and
	study of the effects on the image files.  The intent is to spread
	hard-earned knowledge gained over many years amongst those new to the
	field or a particular piece of equipment, not to threaten anyone's
	proprietary interests, or to substitute for the technical support
	available from vendors that ranges from free to extortionate, and
	excellent to abysmal, depending on who your are dealing with and where
	in the world you are located!

	Please use this information in the spirit in which is intended, and
	where possible contribute whatever you know in order to expand the
	information to cover more vendors and equipment.

    1.2 Types of Formats

	Later sections will deal with the problems of getting the image files
	from the modality to the workstation, but for the moment assume the
	files are there and need to be deciphered.

	Four types of information are generally present in these files:

	   - image data, which may be unmodified or compressed, - patient
	   identification and demographics, - technique information about the
	   exam, series, and slice/image.

	Extracting the image information alone is usually straightforward and is
	described in 1.3.  Dealing with the descriptive information, for example
	to make use of the data for dissemination in a PACS environment, or to
	extract geometry details in order to combine images into 3D datasets, is
	more difficult and requires deeper understanding of how the files are

	There are three basis families of formats that are in popular use:

	   - fixed format, where layout is identical in each file, - block
	   format, where the header contains pointers to information, - tag
	   based format, where each item contains its own length.

	The block format is one of the most popular, though in most cases, the
	early part of the header contains only a limited number of pointers to
	large blocks, the blocks are almost always in the same place and a
	constant length, for standard rather than reformatted images at least,
	and if one doesn't know the specifics of the layout one can get by
	assumming a fixed format.  I presume this reflects the intent of the
	designers to handle future expansion and revision of the format.

	The example par excellence of the tag based format is the ACR/NEMA style
	of data stream, which, though never intended as a file format per se has
	proven useful as model.  See for example the sections dealing with the
	ACR/NEMA standards as well as DICOM (whose creators are about to vote on
	a media interchange format after all this time) and Papyrus.  ACR/NEMA
	style tags are described in more detail elsewhere, but each is
	self-contained and self-describing (at least if you have the appropriate
	data dictionary) and contains its own length, so if you can't interpret
	it you can skip it!  Very convenient.  Most file formats based on this
	scheme are just concatenated series of tags, and apart from having to
	guess the byte order, which is not specified (unlike TIFF which is a
	similar deal for those in the "real" imaging world), and sometimes skip
	a fixed length but short header, are dead easy to handle.

	To identify such a file just do a "strings <file | grep 'ACR-NEMA'" - if
	it is such a file, just look through the start of the hex dump until you
	start to see the characteristic sequentially ordered pairs of 16 bit
	words that identify ACR/NEMA attributes, decide the byte order, et
	voila, you can pipe it into any general ACR/NEMA dumping program to see
	what it contains.  If you see even group tags, they will be described in
	the standard.  If you see odd group tags then they are vendor specific
	and you will have to ask the vendor or correlate them with
	identification information printed on the film until you figure out the
	ones that are important to you.

    1.3 In Desperation - Quick & Dirty Tricks

	Because radiologists, radiographers, technologists, physicists and
	imaging programmers are dedicated long suffering creatures who work long
	hours under adverse conditions for little reward, the vendors in their
	generosity have seen fit to make life a little easier, by almost
	universally putting the image data at the end of the file.  Rarely you
	will see files that are padded out to fixed record size boundaries (eg.
	Vax VMS 512 byte records), and sometimes overlay plane data may be
	stored after the image data.  Furthermore there is almost always an
	option at archive time to allow for storage in an uncompressed and
	totally unadulterated form.  Even in ACR/NEMA the tag for image pixel
	data is numerically the highest and hence the last to appear in the
	sequence which is guaranteed to be sorted.

	They could have screwed us up totally by gratuitously adding variable
	length blocks of other stuff at the end, but the only time I have
	encountered this was on a Siemens Impact with the ACR/NEMA based SPI
	format padded out to 512 bytes.

	In other words, if an image is 256 by 256, uncompressed, and 12-16 bits
	deep (and hence usually, though not always, stored as two bytes per
	pixel), then we all know that the file is going to contain
	256*256*2=131072 bytes of pixel data at the end of the file.  If the
	file is say 145408 bytes long, as all GE Signa 3X/4X files are for
	example, then you need to skip 14336 bytes of header before you get to
	the data.  Presume row by row starting with top left hand corner raster
	order, try both alternatives for byte order, deal with the 16 to 8 bit
	windowing problem, and very soon you have your image on the screen of
	your workstation.

	This technique is so useful, even NIH Image for the Macintosh (an
	excellent must-have free program BTW.) provides a raw import tool to do
	this, and describes it in the manual using the 14336 byte offset!  This
	tool is something that is sadly lacking in most commercial image
	handling programs for non-medical applications, which can't import
	images with more than 8 bits per channel.

	Of course you have to live without the identification, demographic and
	technique information (other than what can be derived from the file name
	in some cases), but for many research and presentation purposes this is
	quite adequate.

	Occasionally one runs into clever files where four 12 bit words are
	packed into three 16 bit words and one goes crazy trying to figure out
	the logic of how they are packed.  The back of the old ACR/NEMA standard
	describes somewhere one way in which this is done.  One should still be
	able to calculate the length easily enough.

	I haven't yet encountered a format that did nasty things like have
	strips of rows seperated by padding ...  I guess we are lucky that most
	images are nice powers of two or even multiples thereof (256,320,512).

	Of course the GE CT 9800 uses perimeter encoding even when DPCM
	compression is not selected, so this technique won't work.

2.  Standard Formats

    2.1 ACR/NEMA 1.0 and 2.0

	ACR/NEMA Standards Publication No.  300-1985 <- ACR/NEMA 1.0 ACR/NEMA
	Standards Publication No.  300-1988 <- ACR/NEMA 2.0 ACR/NEMA Standards
	Publication PS2-1989 <- data compression

	The American College of Radiologists (ACR) and the National Electrical
	Manufacturers Association (NEMA) recognized some time ago the need for
	standards to facilitate multi-vendor connectivity to promote the
	development of PACS and what is now referred to as Wide Area Networking.
	The first such standard was version 1.0 which was released in 1985 as
	ACR/NEMA Standards Publication No.  300-1985, subsequently revised
	several times, then revised again and released as version 2.0 in 1988,
	described in ACR/NEMA Standards Publication No.  300-1988.  There it
	remained until a radically revised and reorganized approach, preserving
	backward compatibility, was released during 1992-1993 as ACR/NEMA
	Standards Publication PS3, also referred to as DICOM 3.

	In the interim, to facilitate the transfer of compressed images, another
	standard described in ACR/NEMA Standards Publication PS2-1989, was
	released which described various means fo extending standard 300-1985 to
	handle compression utilizing a broad range of reversible and
	irreversible schemes.  Though this part of the standard was never
	apparently implemented by anyone, and has been quietly bypassed by those
	working on DICOM 3 compression, it makes very interesting reading and is
	a nice summary of applicable techniques.

	What does one need to know about ACR/NEMA 1.0 and 2.0 ?  The standards
	define a mechanism along the lines of the layered ISO-OSI (Open Systems
	Interconnect) model, with physical, transport/network, session, and
	presentation and application layers.  Unless one actually wants to
	physically connect to a device that supports the unique 50 pin
	point-to-point electrical interface, then one really only needs to be
	aware of how ACR/NEMA implements the presentation and application
	layers, which are described in terms of a "message format".  This
	message format is important to many people, not because anyone seriously
	wants to connect devices in the limited fashion envisaged by these early
	standards, but because many proprietary formats and other de facto
	standards have adopted the ACR/NEMA message format and its corresponding
	data dictionary and extension mechanisms.

	The message format is described in sections 4, 5 and 10 of ACR/NEMA SP
	300-1988 which are summarized briefly here.  Section 6 describes command
	structure which is not really relevant other than that commands are also
	structured in the same way as data and consume part of the data
	dictionary.  You will not encounter command tags in data streams
	("messages") encapsulated in file formats though.

	A message consists of a series of "data elements" each of which contains
	a piece of information.  Each element is described by an "element name"
	consisting of a pair of 16 bit unsigned integers ("group number", "data
	element number").  The data stream is ordered by ascending group number,
	and within each group by ascending data element number.  Each element
	may occur only once in a message.  Even numbered groups describe
	elements defined by the standard.  Odd numbered groups are available for
	use by vendors or users, but must conform to the same structure as
	standard elements.  Following the (group number, data element number)
	pair is a length field that is a 32 bit unsigned even integer that
	describes the number of bytes from the end of the length field to the
	beginning of the next data element.

	The last part of a data element is its value, which is defined by the
	data dictionary to be an ascii (numeric AN or text AT) or binary value
	(BI 16 bit or BD 32 bit).  The values may be single or multiple.
	Multiple ascii values are delimited by the backslash (05CH) character.
	Odd length ascii values are padded with a space (020H).

	For example:

	    0008 0010 000C 0000 4341 2D52 454E 414D
				  3120 302E

	is data element "Recognition Code" because that is what the dictionary
	defines group 0008 element 0010 to be.  The dictionary says it is of
	type AT (ascii text), has a value multiplicity of single and only
	enumerated values are allowed, in this case the ascii string "ACR-NEMA
	2.0".  It is of length 0000000C hex or 12 bytes long.

	The electrical interface is a 16 bit one, and hence even though 32
	binary values are defined to be transmitted least significant word first
	(though the order for the 32 bit length is not actually specified),
	there is no mention in the standard as to how to encapsulate the message
	in an 8 bit world, hence different users and vendors have chosen little
	or big endian schemes.  The new DICOM standard assumes a default little
	endian representation which seems to be the most appropriate considering
	the old definition for 32 bit words, which specified that the least
	significant 16 bit word be transmitted first.

	Hence there are three likely possible byte orders that a vendor
	interpreting the ACR/NEMA standard in a byte oriented world may have

	    - little endian 16 and 32 bit words, as in DICOM 3, - big endian 16
	    and 32 bit words, as in DICOM 3, - big endian 16 bit words, but the
	    least significant half of
	      a 32 bit word is sent first (as per ACR/NEMA 2.0).

	The choice seems to be made usually on the basis of the native byte
	order of integers on the host processor.  Most of the formats I have
	encountered are one of the first two, but I did encounter one from
	Philips that used the last scheme and it drove me crazy for a while,
	until I appreciated the subtlety of it !  I call it "Big Bad Endian"
	format in my implementation that recognizes it, but that may be a value
	judgement on my part :)

	Notice particularly how this design allows one to parse the message even
	if the data dictionary is not complete.  Consider an element that has an
	unrecognized element name.  One cannot interpret the content of the
	element and so has to ignore it.  One doesn't even know whether it
	contains binary or ascii information (this is what DICOM later refers to
	as "implicit representation".  despite this, the length value allows one
	to skip to the next element and proceed.

	Over the years there has been much discussion amongst those who favour
	such implicit dictionary driven schemes, and those who prefer explicit
	representations, including explicit description of the element type
	(binary or ascii, etc.) and even the element description itself!  Some
	would prefer the message to contain something like
	"RecognitionCode='ACR-NEMA 2.0';" for example.  The nuclear medicine
	groups have adopted a de facto standard called Interfile that makes use
	of ACR/NEMA data elements, but uses such a descriptive representation.
	Their argument is that the data stream is much more readable which is
	true enough, and more readily extensible.

	The groups are organized as follows:

	    0000 Command 0008 Identifying 0010 Patient 0018 Acquisition 0020
	    Relationship 0028 Image Presentation 4000 Text 6000-601E (even)
	    Overlay 7FE0 Pixel Data

	Some of the more interesting elements are:

	    (nnnn,0000) BD S Group Length # of bytes in group nnnn (nnnn,4000)
	    AT M Comments

	    (0008,0010) AT S Recognition Code # ACR-NEMA 1.0 or 2.0 (0008,0020)
	    AT S Study Date # (0008,0021) AT S Series Date # (0008,0022) AT S Acquisition Date #
	    (0008,0023) AT S Image Date # (0008,0030) AT S Study Time
	    # (0008,0031) AT S Series Time #
	    (0008,0032) AT S Acquisition Time # (0008,0033) AT S
	    Image Time # (0008,0060) AT S Modality #

	    (0010,0010) AT S Patient Name (0010,0020) AT S Patient ID
	    (0010,0030) AT S Patient Birthdate # (0010,0040) AT S
	    Patient Sex # M, F, O for other (0010,1010) AT S Patient Age # xxxD
	    or W or M or Y

	    (0018,0010) AT M Contrast/Bolus Agent # or NONE (0018,0030) AT M
	    Radionuclide (0018,0050) AN S Slice Thickness # mm (0018,0060) AN M
	    KVP (0018,0080) AN S Repetition Time # ms (0018,0081) AN S Echo Time
	    # ms (0018,0082) AN S Inversion Time # ms (0018,1120) AN S Gantry
	    Tilt # degrees

	    (0020,1040) AT S Position Reference # eg.  iliac crest (0020,1041)
	    AN S Slice Location # in mm (signed)

	    (0028,0010) BI S Rows (0028,0011) BI S Columns (0028,0030) AN M
	    Pixel Size # row\col in mm (0028,0100) BI S Bits Allocated # eg.  12
	    bit for CT (0028,0101) BI S Bits Stored # eg.  16 bit (0028,0102) BI
	    S High Bit # eg.  11 (0028,0103) BI S Pixel Representation # 1
	    signed, 0 unsigned

	    (7FE0,0010) BI M Pixel Data # as described by grp 0028

	The way in which the pixel data is stored can vary tremendously, though
	thankfully most users and vendors use the simple unimaginative scheme
	that is shown above, ie.  1 12 bit pixel stored in the low order part of
	a 16 bit word with no attempt at packing more compactly.  Following are
	some examples shown in Appendix E of the standard.  Note that when one
	adds the little/big endian question the permutations mount!

	Bits Allocated = 16 Bits Stored = 12 High Bit = 11

			  |<------------------ pixel ----------------->|
	    ______________ ______________ ______________ ______________
	    15 12 11 8 7 4 3 0


	Bits Allocated = 16 Bits Stored = 12 High Bit = 15

	   |<------------------ pixel ----------------->|
	    ______________ ______________ ______________ ______________
	    15 12 11 8 7 4 3 0


	Bits Allocated = 12 Bits Stored = 12 High Bit = 11

	   ------ 2 ----->|<------------------ pixel 1 --------------->|
	    ______________ ______________ ______________ ______________
	   | | | | |
	    15 12 11 8 7 4 3 0

	   -------------- 3 ------------>|<------------ 2 --------------
	    ______________ ______________ ______________ ______________
	   | | | | |
	    15 12 11 8 7 4 3 0

	   |<------------------ pixel 4 --------------->|<----- 3 ------
	    ______________ ______________ ______________ ______________
	   | | | | |
	    15 12 11 8 7 4 3 0


	And so on ...  refer to the standard itself for more detail.

The next part is part2 - standard formats (continued).

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