Subject: Medical Image Format FAQ, Part 1/2 Followup-To: alt.image.medical Date: 8 Jul 199

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Path:!hookup!swrinde!sgiblab!a2i!!!not-for-mail From: (David A. Clunie) Newsgroups: alt.image.medical,comp.protocols.dicom,,alt.answers,comp.answers,sci.answers,news.answers Subject: Medical Image Format FAQ, Part 1/2 Followup-To: alt.image.medical Date: 8 Jul 1994 10:50:29 +0300 Organization: Her Master's Voice Lines: 934 Approved: news-answers-request@MIT.EDU Distribution: world Message-ID: <2vj0g5$697@britt.ksapax> Reply-To: (David A. Clunie) NNTP-Posting-Host: britt.ksapax Summary: This posting contains answers to the most Frequently Asked Question on alt.image.medical - how do I convert from image format X from vendor Y to something I can use ? In addition it contains information about various standard formats. Xref: alt.image.medical:1162 comp.protocols.dicom:247 alt.answers:3508 comp.answers:6214 sci.answers:1357 news.answers:22232 Archive-name: medical-image-faq/part1 Posting-Frequency: monthly Last-modified: Fri Jul 8 10:48:34 GMT+0300 1994 Version: 1.01 This message is automatically posted once a month to help readers looking for information about medical image formats. If you don't want to see this posting every month, please add the subject line to your kill file. Contents: part1 - contains index, general information & standard formats part2 - contains information about proprietary formats & hosts Changes this issue: Changed archive name to 'medical-image-faq/partn' at request of mit. Added qsh information. Sparc floating point code bug fixed. Data General network hardware/software. Using the Vax/VMS DUMP utility to encode for ascii transfer. More Siemens information. Philips S5 MRI image data format. Added lunis information. Added mailserver section: ftpmail, interfile, medimagex, nucmed. Changes last issue: Split into two parts. GE Genesis information extended. GE Signa 3X/4X image data format included. Siemens GBS II, Impact, DR information (limited). Picker IQ/PQ CT information (limited). Vax data layout description. More anti-VMS vitriol added. Sparc data layout description. Many FAQs, including this Listing, are available on the archive site in the directory pub/usenet/news.answers. The name under which a FAQ is archived appears in the Archive-name line at the top of the article. There's a mail server on that machine. You send a e-mail message to containing the keyword "help" (without quotes!) in the message body. Note: this FAQ has been formatted as a digest. Many newsreaders can skip to each of the major subsections by pressing ^G. Please direct comments or questions and especially contributions to "" or reply to this article. START OF PART 1 -------- Subject: Index 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 ACR/NEMA DICOM 3.0 2.3 Papyrus 2.4 Interfile V3.3 2.5 Qsh 3. Proprietary Formats 3.1 General 3.1.1 SPI (Standard Product Interconnect) 3.2 CT 3.2.1 General Electric CT 9800 Image data Tape format Raw data CT Advantage - Genesis Image data Archive format Raw data Scitec/Pace 3.2.2 Siemens Somatom DR Somatom Plus Somatom AR 3.2.3 Philips 3.2.4 Picker 3.2.5 Toshiba 3.2.6 Hitachi 3.2.7 Shimadzu 3.2.8 Elscint 3.3 MR 3.3.1 General Electric Signa 3X and 4X Image data Tape format Raw data Signa 5X - Genesis Image data Tape format Raw data Vectra 3.3.2 Siemens GBS II SP/Vision Impact 3.3.3 Philips S5 ACS T5 NT5 & NT15 3.3.4 Picker 3.3.5 Toshiba 3.3.6 Hitachi 3.3.7 Shimadzu 3.3.8 Elscint 4. Host Machines 4.1 Data General 4.1.1 Data Integers Floating Point 4.1.2 Operating System RDOS AOS/VS 4.1.3 Network 4.2 Vax 4.2.1 Data Integers Floating Point 4.2.2 Operating System VMS ULTRIX OSF 4.3 Sun4 - Sparc 4.2.1 Data Integers Floating Point 4.2.2 Operating System 5. Compression Schemes 5.1 Reversible 5.2 Irreversible 5.2.1 Perimeter Encoding 6. Getting Connected 6.1 Tapes 6.2 Ethernet 6.3 Serial Ports 7. Sources of Information 7.1 Vendor Contacts 7.2 Relevant FAQ's 7.3 Source Code 7.4 Commercial Offerings 7.5 FTP sites 7.6 Mailservers 7.7 References 8. Acknowledgements -------- Subject: Introduction 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 more ! 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 constructed. 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 | ______________ ______________ ______________ ______________ |XXXXXXXXXXXXXX| | | | |______________|______________|______________|______________| 15 12 11 8 7 4 3 0 --------------------------- Bits Allocated = 16 Bits Stored = 12 High Bit = 15 |<------------------ pixel ----------------->| ______________ ______________ ______________ ______________ | | | |XXXXXXXXXXXXXX| |______________|______________|______________|______________| 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. 2.2 ACR/NEMA DICOM 3.0 ACR/NEMA Standards Publications No. PS 3.1-1992 <- DICOM 3 - Introduction & Overview No. PS 3.8-1992 <- DICOM 3 - Network Communication Support No. PS 3.2-1993 <- DICOM 3 - Conformance No. PS 3.3-1993 <- DICOM 3 - Information Object Definitions No. PS 3.4-1993 <- DICOM 3 - Service Class Specifications No. PS 3.5-1993 <- DICOM 3 - Data Structures & Encoding No. PS 3.6-1993 <- DICOM 3 - Data Dictionary No. PS 3.7-1993 <- DICOM 3 - Message Exchange No. PS 3.9-1993 <- DICOM 3 - Point-to-Point Communication No. PS 3.10-???? <- DICOM 3 - Media Storage & File Format No. PS 3.11-???? <- DICOM 3 - Media Storage Application Profiles No. PS 3.12-???? <- DICOM 3 - Media Formats & Physical Media DICOM (Digital Imaging and Communications in Medicine) standards are of course the hot topic at every radiological trade show. Unlike previous attempts at developing a standard, this one seems to have the potential to actually achieve its objective, which in a nutshell, is to allow vendors to produce a piece of equipment or software that has a high probability of communicating with devices from other vendors. Where DICOM differs substantially from other attempts, is in defining so called Service-Object Pairs. For instance if a vendor's MR DICOM conformance statement says that it supports an MR Storage Class as a Service Class Provider, and another vendor's workstation says that it supports an MR Storage Class as a Service Class User, and both can connect via TCP/IP over Ethernet, then the two devices will almost certainly be able to talk to each other once they are setup with each others network addresses and so on. The keys to the success of DICOM are the use of standard network facilities for interconnection (TCP/IP and ISO-OSI), a mechanism of association establishment that allows for negotiation of how messages are to be transferred, and an object-oriented specification of Information Objects (ie. data sets) and Service Classes. Of course all this makes for a huge and difficult to read standard, but once the basic concepts are grasped, the standard itself just provides a detailed reference. From the users' and equipment purchasers' points of view the important thing is to be able to read and match up the Conformance Statements from each vendor to see if two pieces of equipment will talk. Just being able to communicate and transfer information is of course not sufficient - these are only tools to help construct a total system with useful functionality. Because a workstation can pull an image off an MRI scanner doesn't mean it knows when to do it, when the image has become available, to which patient it belongs, and where it is subsequently archived, not to mention notifying the Radiology or Hospital Information System (RIS/HIS) when such a task has been performed. In other words DICOM Conformance does not guarantee functionality, it only facilitates connectivity. In otherwords, don't get too carried away with espousing the virtues of DICOM, demanding it from vendors, and expecting it to be the panacea to create a useful multi-vendor environment. Fred Prior ( has come up with the concept of a User Conformance Statement to be generated by purchasers and to be satisfied by vendors. The idea is that one describes what one expects and hence gives the vendor a chance to realistically satisfy the buyer ! Of course each such statement must be tailored to the user's needs, and simply stapling a copy of Fred's statement to a Request For Proposals is not going to achieve the desired objective. Caveat empor. To get more information about DICOM: - Purchase the standards from NEMA (address below) when they become available around July 1994. - Ftp the final versions of the drafts in electronic form one of the sites described below. - Follow the Usenet group comp.protocols.dicom. - Get a copy of "Understanding DICOM 3.0" $12.50 from Kodak. - Insist that your existing and potential vendors supply you with DICOM conformance statements before you upgrade or purchase, and don't buy until you know what they mean. Don't take no for an answer !!!! What is all this doing in an FAQ about medical image formats you ask ? Well first of all, in many ways DICOM 3.0 will solve future connectivity problems, if not provide functional solutions to common problems. Hence actually getting the images from point A to B is going to be easier if everyone conforms. Furthermore, for those of us with old equipment, interfacing it to new DICOM conforming equipment is going to be a problem. In otherwords old network solutions and file formats are going to have to be transformed if they are going to communicate unidirectionally or bidirectionally with DICOM 3.0 nodes. One is still faced with the same old questions of how does one move the data and how does one interpret it. The specifics of the DICOM message format are very similar to the previous versions of ACR/NEMA on which it is based. The data dictionary is greatly extended, and certain data elements have been "retired" but can be ignored gracefully if present. The message itself can now be transmitted as a byte stream over networks, rather than using a point-to-point paradigm excusively (though the old point-to-point interface is available). This message can be encoded in various different Transfer Syntaxes for transmission. When two devices ("Application Entities" or AE) begin to establish an "Association", they negotiate an appropriate transfer syntax. They may choose an Explicit Big-Endian Transfer Syntax in which integers are encoded as big-endian and where each data element includes a specific field that says "I am an unsigned 16 bit integer" or "I am an ascii floating-point number", or alternatively they can fall back on the default transfer syntax which every AE must support, the Implicit Little-Endian Transfer Syntax which is just the same as an old ACR/NEMA message with the byte order defined once and for all. This is all very well if you are using DICOM as it was originally envisaged - talking over a network, negotiating an association, and determining what Transfer Syntax to use. What if one wants to store a DICOM message in a file though ? Who is to say which transfer syntax one will use to encode it offline ? One approach, used for example by the Central Test Node software produced by Mallinkrodt and used in the RSNA Inforad demonstrations, is just to store it in the default little-endian implicit syntax and be done with it. This is obviously not good enough if one is going to be mailing tapes, floppies and optical disks between sites and vendors though, and hence the DICOM group decided to define a "Media Storage & File Format" part of the standard, the new Chapter 10 which is about to be or has just been voted on. Amongst other things, this new part defines a generic DICOM file format that contains a brief header, the "DICOM File Meta Information Header" which contains a 128 byte preamble (that the user can fill with anything), a 4 byte DICOM prefix "DICM", then a short DICOM format message that contains newly defined elements of group 0002 in the default Implicit Little Endian Transfer Syntax, which uniquely identify the data set as well as specifying the Transfer Syntax for the rest of the file. The rest of the message must specify a single SOP instance which can of course contain multiple images as folders if necessary. The length of the brief message in the Meta Header is specified in the first data element as usual, the group length. So what choices of Transfer Syntax does one have and why all the fuss ? Well the biggest distinction is between implicit and explicit representation which allows for multiple possible representations for a single element, in theory at least, and perhaps allows one to make more of an unknown data element than one otherwise could perhaps. Some purists (and Interfile people) would argue that the element should be identified descriptively, and there is nothing to stop someone from defining their own private Transfer Syntax that does just that (what a heretical thought, wash my mouth out with soap). With regard to the little vs. big endian debate I can't see what the fuss is about, as it can't really be a serious performance issue. Perhaps more importantly in the long run, the Transfer Syntax mechanism provides a means for encapsulating compressed data streams, without having to deal with the vagaries and mechanics of compression in the standard itself. For example, if DICOM version 3.0, in addition to the "normal" Transfer Syntaxes, a series are defined to correspond to each of the Joint Photographic Experts Group (JPEG) processes. Each one of these Transfer Syntaxes encodes data elements in the normal way, except for the image pixel data, which is defined to be encoded as a valid and self-contained JPEG byte stream. Both reversible and irreversible processes of various types are provided for, without having to mess with the intricacies of encoding the various tables and parameters that JPEG processes require. Presumably a display application that supports such a Transfer Syntax will just chop out the byte stream, pass it to the relevant JPEG decode, and get an uncompressed image back. More importantly, an archive server can store the image and retrieve it without ever having to know anything about how the image pixel data is encoded. Contrast this approach with that taken by those defining the TIFF (Tagged Image File Format) for general imaging and page layout applications. In their version 6.0 standard they attempted to disassemble the JPEG stream into its various components and assign each to a specific tag. Unfortunately this proved to be unworkable after the standard was disseminated and they have gone back to the drawing board. Now one may not like the JPEG standard, but one cannot argue with the fact that the scheme is workable, and a readily available means of reversible compression has been incorporated painlessly. How effective a compression scheme this is remains to be determined, and whether or not the irreversible modes gain wide acceptance will be dictated by the usual medico-legal paranoia that prevails in the United States, but the option is there for those who want to take it up. There is of course no reason why private compression schemes cannot be readily incorporated using this "encapsulation" mechanism, and to preserve bandwidth this will undoubtedly occur. This will not compromise compatibility though, as one can always fall back to a default, uncompressed Transfer Syntax. The DICOM Working Group on compression will undoubtedly bring out new possibilities. In order to identify all these various syntaxes, information objects, and so on, DICOM has adopted the ISO concept of the Unique Identifier (UID) which is a text string of numbers and periods with a unique root for each organization that is registered with ISO and various organizations that in turn register others in a hierarchical fashion. For example 1.2.840.10008.1.2 is defined as the Implicit VR Little Endian Transfer Syntax. The 1 identifies ISO, the 2 is the ISO member body branch, the 840 is the specific member body country code, in this case ANSI, and the 10008 is registered by ANSI to NEMA for DICOM. UID's are also used to uniqely identify non-DICOM specific things, such as information objects. These are constructed from a prefix registered to the supplier or vendor or site, and a unique suffix that may be generated from say a date and time stamp (which is not to be parsed). For example an instance of a CT information object might have a UID of 1.2.840.123456.002.999999.940623.170717 where a (presumably US) vendor registered 123456, and the modality generated a unique suffix based on its device number, patient hospital id, date and time, which have no other significance other than to create a unique suffix. The other important new concept that DICOM introduced was the concept of Information Objects. In the previous ACR/NEMA standard, though modalities were identified by a specific data element, and though there were rules about which data elements were mandatory, conditional or optional in ceratin settings, the concept was relatively loosely defined. Presumably in order to provide a mechanism to allow conformance to be specified and hence ensure interoperability, various Information Objects are defined that are composed of sets of Modules, each module containing a specific set of data elements that are present or absent according to specific rules. For example, a CT Image Information Object contains amongst others, a Patient module, a General Equipment module, a CT Image module, and an Image Pixel module. An MR Image Information module would contain all of these except the CT Image module which would be replaced by an MR Image module. Clearly one needs descriptive information about a CT image that is different from an MR image, yet the commonality of the image pixel data and the patient information is recognized by this model. Hence, as described earlier, one can define pairs of Information Objects and Services that operate on such objects (Storage, Query/Retrieve, etc.) and one gets SOP classes and instances. All very object oriented and initially confusing perhaps, but it provides a mechanism for specifying conformance. From the point of view of an interpreters of a DICOM compatible data stream this means that for a certain instance of an Information Object, certain information is guaranteed to be in there, which is nice. As a creator of such a data stream, one must ensure that one follows all the rules to make sure that all the data elements from all the necessary modules are present. Having done so one then just throws all the data elements together, sorts them into ascending order by group and element order, and pumps them out. It is a shame that the data stream itself doesn't reflect the underlying order in the Information Objects, but I guess they had to maintain backward compatibility, hence this little bit of ugliness. This gets worse when one considers how to put more than one object in a folder inside another object. At this point I am tempted to include more details of various different modules, data elements and transfer syntaxes, as well as the TCP/IP mechanism for connection. However all this information is in the standard itself which is readily available electronically from the ftp sites, and in the interests of brevity I will not succumb to temptation at this time. 2.3 Papyrus Papyrus is an image file format based on ACR/NEMA version 2.0. I don't have much information about it yet, but what I do know, gleaned from Usenet and a presentation at SCAR 94 is: - it is from Switzerland, - there is a library of tools available for handling it, - it allows multiple images/file, - it has something to do with the European RACE Telemed project, - it stores 16 bit integers as big-endian, and that is all for the moment ! Someone is sending me more information Real Soon Now so stay tuned. 2.4 Interfile V3.3 Interfile is a "file format for the exchange of nuclear medicine image data" created I gather under the auspices of the American Association of Physicists in Medicine (AAPM) for the purpose of transfer of images of quality control phantoms, and has been subsequently used for clinical work (please correct me if I am wrong Trevor). It specifies a file format composed of ascii "key-value" pairs and a data dictionary of keys. The binary image data may be contained in the same file as the "administrative information", or in a separate file pointed to by a "name of data file" key. Image data may be binary integers, IEEE floating point values, or ascii and the byte order is specified by a key "imagedata byte order". The order of keys is defined by the Interfile syntax which is more sophisticated than a simple list of keys, allowing for groups, conditionals and loops to dictate the order of key-value pairs. Conformance to the Interfile standard is informally described in terms of which types of image data types, pixel types, multiple windows, special Interfile features including curves, and restriction to various maximum recommended limits. Interfile is specifically NOT a communications protocol and strictly deals with offline files. There are efforts to extend Interfile to include modalities other than nuclear medicine, as well as to keep ACR/NEMA and Interfile data dictionaries in some kind of harmony. A sample list of Interfile 3.3 key-value pairs is shown here to give you some idea of the flavor of the format. The example is culled from part of a Static study in the Interfile standard document and is not complete: !INTERFILE := !imaging modality :=nucmed !version of keys :=3.3 data description :=static patient name :=joe doe !patient ID :=12345 patient dob :=1968:08:21 patient sex :=M !study ID :=test exam type :=test data compression :=none !image number :=1 !matrix size [1] :=64 !matrix size [2] :=64 !number format :=signed integer !number of bytes per pixel :=2 !image duration (sec) :=100 image start time :=10:20: 0 total counts :=8512 !END OF INTERFILE := One can see how easy such a format would be to extend, as well as how it is readable and almost useable without reference to any standard document or data dictionary. Undoubtedly ACR/NEMA DICOM 3.0 to Interfile translators will soon proliferate in view of the fact that many Nuclear Medicine vendors supply Interfile translators at present. To get hold of the Interfile 3.3 standard by ftp, see the sources and contacts listed later in this document. 2.5 Qsh Qsh is a family of programs for manipulating images, and it defines an intermediate file format. The following information was derived with the help of one of the authors (Chip Maguire ): Uses an ASCII key-value-pair (KVP sic.) system, based on the AAPM Report #10 proposal. This format influenced both Interfile and ACR-NEMA (DICOM). The file format is referred to as "IMAGE" in some of their articles (see references). The header and the image data are stored as two separate files with extensions *.qhd and *.qim respectively. Qsh is available by anonymous ftp (see Sources section). This is a seriously large tar file, including as it does some sample images, and lots of source code, as well as some post-script documents. Subtrees are available as separate tar files. QSH's Motif-based menu system (qmenu) will work with OpenWindows 3.0 if SUN patch number 100444-54 for SUNOS 4.1.3 rev. A is applied. The patch is available from ( The image access subroutines take the same parameters as the older /usr/image package from UNC, however, the actual subroutines support the qsh KVP and image data files. The frame buffer access subroutines take the same parameters as the Univ. of Utah software (of the mid. 1970s). The design is based on the use of a virtual frame buffer which is then implemented via a library for a specific frame buffer. There exists a version of the the display routines for X11. Conversions are not supported any longer, instead there is a commercial product called Interformat. Interformat includes a qsh to Interfile conversion, along with DICOM to qsh, and many others. Information is available from David Reddy ( (see Sources section). [Editorial note: this seems a bit of a shame to me - hopefully the current distribution still includes the old conversion stuff even if it is not supported as there were lots of handy bits of information there, particularly on driving tape drives. DAC.] The authors of the qsh package are: Gerald Q. (Chip) Maguire ( Marilyn E Noz (noz@nucmed.NYU.EDU) The following references are helpful in understanding the philosophy behind the file format, and are included in postscript form in the qsh ftp distribution: @Article[noz88b, Key=, Author=, Title=, Journal=, volume=<27>, month=, Year=<1988>, Pages=<229-240> ] @Article[maguire89e, Key=, Author=, Title=, Journal=, volume=<16>, month=, year=<1989>, pages=<818-823>, comment= ] END OF PART 1 -- David A. Clunie ( In sunny Riyadh, Saudi Arabia. "I must see your DICOM 3 conformance statement before I buy."


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