Path: senator-bedfellow.mit.edu!bloom-beacon.mit.edu!newsfeed.stanford.edu!headwall.stanford.edu!newshub.sdsu.edu!news-hog.berkeley.edu!ucberkeley!news2.epix.net!news1.epix.net!dclunie.com Newsgroups: alt.image.medical,comp.protocols.dicom,sci.data.formats,alt.answers,comp.answers,sci.answers,news.answers Message-ID: <20031221091625.3015.1@dclunie.com> Expires: 21 Jan 2004 00:00:00 GMT Subject: Medical Image Format FAQ, Part 1/8 From: dclunie@dclunie.com (David A. Clunie) Followup-To: alt.image.medical Reply-To: dclunie@dclunie.com (David A. Clunie) Approved: news-answers-request@MIT.EDU 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. Lines: 729 Date: Sun, 21 Dec 2003 14:16:25 GMT NNTP-Posting-Host: 216.37.230.197 X-Complaints-To: abuse@epix.net X-Trace: news1.epix.net 1072016185 216.37.230.197 (Sun, 21 Dec 2003 09:16:25 EST) NNTP-Posting-Date: Sun, 21 Dec 2003 09:16:25 EST Xref: senator-bedfellow.mit.edu alt.image.medical:12454 comp.protocols.dicom:11710 sci.data.formats:3059 alt.answers:70768 comp.answers:55773 sci.answers:15694 news.answers:263499 Archive-name: medical-image-faq/part1 Posting-Frequency: monthly Last-modified: Sun Dec 21 09:16:25 EST 2003 Version: 4.26 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 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 Tools that describe and convert many of the formats described in this document are available in the dicom3tools package from "http://www.dclunie.com/dicom3tools.html". A web browsable version of this FAQ is available at: "http://www.dclunie.com/medical-image-faq/html/" or at the mirror sites: "http://www.focus-fr.com/links/faq/medical/" "http://www.focus-fr.com/links/" Html and text forms of the FAQ are available at (postscript and pdf no longer provided): "http://www.dclunie.com/medical-image-faq/". Many FAQs, including this Listing, are available on the archive sites: "ftp://rtfm.mit.edu/pub/usenet/news.answers/medical-image-faq/" "http://www.faqs.org/faqs/medical-image-faq/part1/" "http://www.cs.uu.nl/wais/html/na-dir/medical-image-faq/part1.html" "ftp://ftp.univ-lille1.fr/pub/faq/medical-image-faq/part1" "http://www.pasteur.fr/infosci/FAQ/medical-image-faq/part1" "http://www.panther.net/FAQ/medical-image-faq/part1" "http://faqs.jmas.co.jp/FAQs/medical-image-faq/part1" "http://www.han.de/usenet/medical-image-faq/part1.gz" "http://www.landfield.com/faqs/medical-image-faq/part1/" 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 the FAQ archives. You send a e-mail message to mail-server@rtfm.mit.edu containing the keyword "help" (without quotes!) in the message body. To fetch this particular FAQ send a message with the following body: send usenet/news.answers/medical-image-faq/part1 ... send usenet/news.answers/medical-image-faq/part8 Please direct comments or questions and especially contributions to "mailto:dclunie@dclunie.com" or reply to this article. All unknown formats and test images gratefully accepted. Changes this issue Add Chinese and Korean Visible Human sites Add IntuitiveImaging conformance statement site Add PACSGear document scanning conformance statement site Remove email addresses to minimize spam Update Tiani conformance statement link Add UniPACS site Extensively revise conformance statement links Remove xray.psu dead links Reorganize toolkit summary, and remove lots of dead toolkit links Add Trevor Morgan's dicomlib toolkit Add JDCM Java DICOM Toolkit Add PixelMed Java DICOM Toolkit Tidy up Medigration info Tidy up OFFIS urls Add CDMEDICSPACSWEB site Add Conquest DICOM site Add JiveX site Update UCDMC sites to http from ftp Update DICOM image sample sites Update XMedCon PET format convertor site Update ITU T.81 text site Add transfer syntax determination explanatuon and code Add Madena viewer site Add idoimaging index site Add iRad Mac viewer site Add IBM conformance statement site Comment that R Hindel and book no longer contactable Add free PACS web site Add Apteryx Java Image I/O Plugin site Update Escape QT site Add YourDICOM site Add MRIConvert site Add explanation of DICOM image orientation Update JPEG 2000 resources Clean up a lot of conformance statement links Update UID registration, and elaborate on description Revise structured reporting resources, and add new web site Add dicomworks site Add Almacom's J2K codec site Update Mark Nelson's data compression library site Update TIFF spec site at Adobe Update ALI conformance site Add Sanders ViewPlus site Update MacAngioView site Add display performance section and AAPM TG18 reference Tidy up part 7 indentation of compression/jpeg links Update VMS tools site Update Kodak conformance statement site Add CardioVista viewer Add sites about reading DICOM in MATLAB Fix IHE MESA tools site reference Add Analog Devices J2K chip Changes last issue Add Tiani Java Image Archive Application with source code Tidy up MultiTech site Add Sante Viewer and Anonymizer site Update MedX site Update bicubic spline interpolation site Update Analyze format sites Add SPM site Update Tiani conformance statement site Add J2K book reference Add Kakadu J2K codec site Update MultiTech Solutions web site Cull out dead links to image sites Update ANSI UID registration address Add InviWeb DicomWorks site Update mirror sites list Add Xinapse software and consulting site Update unuid pathology image site Update Interfile resources Add IHE and MESA tools sites Add DICOM SR sample sites Add reViewMD PocketPC DICOM viewer site Add RMIT Digital Radiography page Update TrueVIEW URL Add NIH etdips 3D software site Add Kitware vtk site Add Konica images site Add ECRI DICOM Compatability Analysis Form site Add Marianne's DicomEdit site Add MedicView site 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 3.1.2.1 Siemens Vax/VMS 3.1.2.2 Siemens Sparc SunOS 3.1.2.2.1 Starting up 3.1.2.2.2 Getting a console 3.1.2.2.3 Native images 3.1.2.2.4 Exporting images 3.1.2.2.5 Physical connection 3.1.2.2.6 Archive devices 3.1.2.2.7 Becoming root 3.1.2.2.8 Reset 3.2 CT - Proprietary Formats 3.2.1 General Electric CT 3.2.1.1 GE CT 9800 3.2.1.1.1 GE CT 9800 Image data 3.2.1.1.2 GE CT 9800 Tape format 3.2.1.1.3 GE CT 9800 Raw data MR 3.2.1.2 GE CT Advantage - Genesis 3.2.1.2.1 GE CT Advantage Image data 3.2.1.2.2 GE CT Advantage Archive format 3.2.1.2.3 GE CT Advantage Raw data 3.2.1.3 GE CT Pace 3.2.1.4 GE CT Sytec 3.2.1.5 GE CTI 3.2.2 Siemens CT 3.2.2.1 Siemens Somatom DR 3.2.2.2 Siemens Somatom Plus 3.2.2.3 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 3.3.1.1 GE MR Signa 3.x,4.x 3.3.1.1.1 GE MR Signa 3.x,4.x Image data 3.3.1.1.2 GE MR Signa 3.x,4.x Tape format 3.3.1.1.3 GE MR Signa 3.x,4.x Raw data 3.3.1.2 GE MR Signa 5.x - Genesis 3.3.1.2.1 GE MR Signa 5.x Image data 3.3.1.2.2 GE MR Signa 5.x Archive format 3.3.1.2.3 GE MR Signa 5.x Raw data 3.3.1.3 GE MR Max 3.3.1.4 GE MR Vectra 3.3.2 Siemens MR 3.3.2.1 Siemens Magnetom GBS/GBS II 3.3.2.1.1 Siemens Magnetom GBS/GBS II Native Format 3.3.2.1.2 Siemens Magnetom GBS/GBS II SPI Format 3.3.2.2 Siemens Magnetom SP 3.3.2.2.1 Siemens Magnetom SP Native Format 3.3.2.2.2 Siemens Magnetom SP SPI Format 3.3.2.3 Siemens Magnetom Impact 3.3.2.3.1 Siemens Magnetom Impact Native Format 3.3.2.3.2 Siemens Magnetom Impact SPI Format 3.3.2.4 Siemens Magnetom Vision 3.3.2.4.1 Siemens Magnetom Vision Native Format 3.3.2.4.2 Siemens Magnetom Vision SPI Format 3.3.3 Philips MR 3.3.3.1 Philips Gyroscan S5 3.3.3.2 Philips Gyroscan ACS 3.3.3.3 Philips Gyroscan T5 3.3.3.4 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 3.4.1.1 Gyroview 3.4.2 GE Workstations 3.4.2.1 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 4.1.1.1 Data General Integers 4.1.1.2 Data General Floating Point 4.1.2 Data General Operating System 4.1.2.1 Data General RDOS 4.1.2.2 Data General AOS/VS 4.1.3 Data General Network 4.2 Vax 4.2.1 Vax Data 4.2.1.1 Vax Integers 4.2.1.2 Vax Floating Point 4.2.1.3 Vax Strings 4.2.2 Vax Operating System 4.2.2.1 Vax VMS 4.2.2.2 ULTRIX 4.2.2.3 OSF 4.3 Sun - Sun3 68000 and Sun4 Sparc 4.3.1 Sun Data 4.3.1.1 Sun Integers 4.3.1.2 Sun Floating Point 4.3.1.3 Sun Strings 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 Sources 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 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. The next part is part2 - standard formats (continued).