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Expires: 21 Jan 2004 00:00:00 GMT
Subject: Medical Image Format FAQ, Part 2/8
From:
[email protected] (David A. Clunie)
Followup-To: alt.image.medical
Reply-To:
[email protected] (David A. Clunie)
Approved:
[email protected]
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.
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Date: Sun, 21 Dec 2003 14:16:30 GMT
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Version: 4.26
2.2 ACR/NEMA DICOM 3.0
ACR/NEMA Standards Publications
PS 3.1 <- DICOM 3 - Introduction & Overview PS 3.8 <- DICOM 3 -
Network Communication Support
PS 3.2 <- DICOM 3 - Conformance PS 3.3 <- DICOM 3 - Information
Object Definitions PS 3.4 <- DICOM 3 - Service Class Specifications
PS 3.5 <- DICOM 3 - Data Structures & Encoding PS 3.6 <- DICOM 3 -
Data Dictionary PS 3.7 <- DICOM 3 - Message Exchange PS 3.9 <- DICOM
3 - Point-to-Point Communication
PS 3.10 <- DICOM 3 - Media Storage & File Format PS 3.11 <- DICOM 3
- Media Storage Application Profiles PS 3.12 <- DICOM 3 - Media
Formats & Physical Media
PS 3.13 <- DICOM 3 - Print Management Point-to-Point Communication
Support PS 3.14 <- DICOM 3 - Grayscale Standard Display Function PS
3.15 <- DICOM 3 - Security Profiles PS 3.16 <- DICOM 3 - Content
Mapping Resource (DCMR)
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.
To get more information about DICOM:
- Purchase the standards from NEMA.
- 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 Parts 10, 11 and 12 which have recently passed their
ballot and should be available in final form from NEMA soon.
Amongst other things, Part 10 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 a specified 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. The length of the brief message in the
Meta Information Header is specified in the first data element as usual,
the group length.
Originally the draft of Part 10 specified the default Implicit Value
Representation Little Endian Transfer Syntax as the DICOM File Meta
Information Header Transfer Syntax, which is in keeping with the concept
that it is the default for all other parts of the standard. The final
text fortunately changed this to Explicit Value Representation Little
Endian Transfer Syntax.
So what choices of Transfer Syntax does one have and why all the fuss ?
Well the biggest distinction is between implicit and explicit value
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.
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. Though originally
every conceivable JPEG (ISO 10918-1) compression process was defined in
the standard, recently all but the most commonly used (8 and 12 bit DCT
lossy huffman and 16 bit lossless huffman) have been retired. 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. More recently, JPEG-LS and JPEG 2000 have
also been added to the standard. RLE (Run Length Encoded) compression,
using the TIFF PackBits mechanism, is also present in the standard and
is used for Ultrasound applications (only, as far as I know).
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. What DICOM calls "UIDs" are referred to in the ISO
OSI world as Object Identifiers (OIDs).
UIDs 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
1.2.840.123456.2.999999.940623.170717 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. Each vendor of
a DICOM implementation needs a UID root from which to begin generating
their own UIDs. See UID - Getting a Registered Organization Number for
a DICOM UID Root for details. It is said that Joint ISO-ITU root form
of "2.16.country" is currently preferred over the "1.country" form of
the root, which is something to bear in mind when building your own root
once you are a registered number. Picker for example uses
"2.16.840.1.113662" as their root. GE uses "1.2.840.113619". The "840"
is the country code for US (there is an assumption that there is one
member body per country responsible for registration) using ISO 3166
numeric country codes. I am not sure why there is a "1" after the
"2.16.840", but one does not seem to need to add a "1" after "1.2.840"
using the ISO registration scheme. I am also not sure if the "1" after
the "840" is a US thing only for joint registrations, or whether other
countries use the "1" also. Note that one does NOT zero-pad UID
components, hence the three-letter ISO 3166 code for Brazil of "076"
would actually be used as "76", e.g. "1.2.76.xxxxxx". This is
something to take great care with when generating the unique suffix for
a particular UID (e.g. don't use serial number "002456" but "2456"
instead).
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, copies of which are readily available electronically
from ftp sites, and in the interests of brevity I will not succumb to
temptation at this time.
2.2.1 Localizer lines on DICOM images
A specific topic that is frequently asked in comp.protocols.dicom is
how to use display an image
of a "localizer" (or "scout" or "scanogram" or "topogram" depending on your
vendor) that has the "lines" corresponding to orthogonal images displayed on it.
This applies both in the case where the orthogonal images were "graphically
prescribed" from the localizer as well as when one just wants to see the
location of images that happen to be orthogonal. In the case of CT images, the
localizer is usually a specific image that is not really a cross-section but a
projection image. In the case of MR one or more sagittal or coronal images are
usually obtained from which axial images are prescribed, and so on. The problem
of "posting" the location of the orthogonal images on a localizer involves:
-Determining which image or images is/are the localizer for a particular
set of images: some vendors send this information in the "Referenced Image
Sequence" attribute, in the case of CT it may simply be an image with an
"Image Type" value 3 of "LOCALIZER" (this doesn't apply to MR) and the
same Frame of Reference UID, and in other cases one just has to search the
entire set of images and find other likely candidates that are orthogonal
or close to it based on "Image Orientation(Patient)". -Having identified
a localizer and a list of images whose locations are to be "posted",
drawing the appropriate lines: there are two approaches that are
fundamentally different conceptually. One can either determine the
intersection between the planes and extents of the localizer and the
orthogonal image, or one can project the boundaries of the orthogonal
image onto the plane of the localizer.
The problem with the "intersection" approach is that no such intersection
may exist. For example, CT localizers are theoretically of infinite
thickness, they are projections not slices, and hence the concept of
intersection does not apply. Even in the case of orthogonal slices, the
boundaries of one slice may not intersect the orthogonal slice at all.
The users requirement is really not to show the intersection, but rather
to "project" the boundaries of a slice onto the plane of the localizer, as
if it were viewed from a position along the normal to the plane of the
localizer. For the purposes of simplicity, perspective is ignored.
Strictly speaking, the projected boundaries form a polygon, but if the
slices are truly orthogonal the polygon will appear as a straight line
(which is what most users expect to see).
The approach I use is to perform a parallel projection of the plane and
extent of the source slice onto the plane of the target
localizer image. One can think of various ways of calculating angles between
planes, dropping normals, etc., but there is a simple approach ...
If one considers the localizer plane as a "viewport" onto the DICOM 3D
coordinate space, then that viewport is described by
its origin, its row unit vector, column unit vector and a normal unit vector
(derived from the row and column vectors by taking the cross product). Now if
one moves the origin to 0,0,0 and rotates this viewing plane such that the row
vector is in the +X direction, the column vector the +Y direction, and the
normal in the +Z direction, then one has a situation where the X coordinate now
represents a column offset in mm from the localizer's top left hand corner, and
the Y coordinate now represents a row offset in mm from the localizer's top
left hand corner, and the Z coordinate can be ignored. One can then convert
the X and Y mm offsets into pixel offsets using the pixel spacing of the
localizer image.
This trick is neat, because the actual rotations can be specified
entirely using the direction cosines that are the row,
column and normal unit vectors, without having to figure out any angles, arc
cosines and sines, which octant of the 3D space one is dealing with, etc.
Indeed, simplified it looks like:
dst_nrm_dircos_x = dst_row_dircos_y * dst_col_dircos_z - dst_row_dircos_z *
dst_col_dircos_y; dst_nrm_dircos_y = dst_row_dircos_z * dst_col_dircos_x -
dst_row_dircos_x * dst_col_dircos_z; dst_nrm_dircos_z = dst_row_dircos_x *
dst_col_dircos_y - dst_row_dircos_y * dst_col_dircos_x;
src_pos_x -= dst_pos_x; src_pos_y -= dst_pos_y; src_pos_z -= dst_pos_z;
dst_pos_x = dst_row_dircos_x * src_pos_x
+ dst_row_dircos_y * src_pos_y + dst_row_dircos_z * src_pos_z;
dst_pos_y = dst_col_dircos_x * src_pos_x
+ dst_col_dircos_y * src_pos_y + dst_col_dircos_z * src_pos_z;
dst_pos_z = dst_nrm_dircos_x * src_pos_x
+ dst_nrm_dircos_y * src_pos_y + dst_nrm_dircos_z * src_pos_z;
The traditional homogeneous transformation matrix form of this is:
[ dst_row_dircos_x dst_row_dircos_y dst_row_dircos_z -dst_pos_x ] [
dst_col_dircos_x dst_col_dircos_y dst_col_dircos_z -dst_pos_y ] [
dst_nrm_dircos_x dst_nrm_dircos_y dst_nrm_dircos_z -dst_pos_z ] [ 0 0 0 1 ]
So this tells you how to transform arbitrary 3D points into localizer
pixel offset space (which then obviously need to be
clipped to the localizer boundaries for drawing), but which points to draw ?
My approach is to project the square that is the bounding box of the
source image (i.e. lines joining the TLHC,
TRHC,BRHC and BLHC of the slice). That way, if the slice is orthogonal to the
localizer the square will project as a single line (i.e. all four lines will
pile up on top of each other), and if it is not, some sort of rectangle or
trapezoid will be drawn. I rather like the effect and it provides a general
solution, though looks messy with a lot of slices with funky angulations.
Other possibilities are just draw the longest projected side, draw a diagonal,
etc.
Do not get too carried away with the precision of the resulting image.
There is some controversy as to whether or not the coordinates in Image
Position (Patient) represent the center of the slice or the edge of it,
and if the edge which edge (leading or trailing with respect to scan
"direction", top or bottom with respect to some axis, etc.). Obviously
the center is the most sensible choice but you cannot guarantee this
(though a recent CP to the standard specifies that it is in fact the
center of the slice - see CP 212). Just be aware that the displayed lines
(and recorded location) may be +/- the slice thickness (or perhaps
spacing) with respect to the orthogonal localizer image.
Do not forget to check that the Frame of Reference UID is the same for
both the localizer and the orthogonal images to be posted. If they are
different one cannot assume the coordinates and vectors are using the same
coordinate space.
Finally, some vendors (especially on older scanners) provide the user with
an ability to post the localizer on the acquisition device and to save
that image, either as a secondary capture object with the lines burned
into the pixel data, or using some form of overlay. There is considerable
variation in the choice of overlay mechanism to use, and not very
consistent support for overlays in other vendors workstations. This leads
to frustrated users who can't see the lines on third party workstations
even though they are supposed to be there. Hopefully in future vendors
will consistently make use of the new Grayscale Softcopy Presentation
State Storage objects to store such graphics, and to fill in "Referenced
Image Sequence" to allow workstations to post the localizers themselves
without hunting for plausible candidates. The IHE Technical Framework for
Year 3 specifies that Referenced Image Sequence shall be used and burned
in lines shall not, which hopefully provides direction for new devices.
There are various implementations of this and other algorithms that may be
of interest at the following sites:
-
http://www.dclunie.com/dicom3tools.html in my dicom3tools: look for
"appsrc/dctools/dcpost.cc" -
http://www.dclunie.com/dicom3tools/workinprogress/dcpost.cc dcpost.cc
(won't compile by itself, but shows the algorithm) -
ftp://ftp.charm.net/pub/usr/home2/dcsipo/slices.ZIP from Dee Csipo -
http://www.tiani.com/JDicom/out/scouts4j.zip from Gunter Zeilinger (Java)
-
http://www.tiani.com/JDicom/out/scouts4cxx.zip from Gunter Zeilinger
(C++)
2.2.2 Orientation of DICOM images
Another question that is frequently asked in comp.protocols.dicom is
how to determine which side of an image is which (e.g. left, right)
and so on. The short answer is that for projection radiographs this
is specified explicitly using the Patient Orientation attribute, and
for cross-sectional images it needs to be derived from the Image
Orientation (Patient) direction cosines. In the standard these are
explained as follows:
-"C.7.6.1.1.1 Patient Orientation.
The Patient Orientation (0020,0020) relative to the image plane shall be
specified by two values that designate the anatomical direction of the positive
row axis (left to right) and the positive column axis (top to bottom). The
first entry is the direction of the rows, given by the direction of the last
pixel in the first row from the first pixel in that row. The second entry is
the direction of the columns, given by the direction of the last pixel in the
first column from the first pixel in that column.
Anatomical direction shall be designated by the capital letters: A (anterior), P
(posterior), R (right), L (left), H (head), F (foot). Each value of the
orientation attribute shall contain at least one of these characters. If
refinements in the orientation descriptions are to be specified, then they shall
be designated by one or two additional letters in each value. Within each
value, the letters shall be ordered with the principal orientation designated in
the first character."
-"C.7.6.2.1.1 Image Position And Image Orientation.
The Image Position (0020,0032) specifies the x, y, and z coordinates of the
upper left hand corner of the image; it is the center of the first voxel
transmitted. Image Orientation (0020,0037) specifies the direction cosines of
the first row and the first column with respect to the patient. These
Attributes shall be provide as a pair. Row value for the x, y, and z axes
respectively followed by the Column value for
the x, y, and z axes respectively.
The direction of the axes is defined fully by the patient's orientation. The
x-axis is increasing to the left hand side of the patient. The y-axis is
increasing to the posterior side of the patient. The z-axis is increasing
toward the head of the patient.
The patient based coordinate system is a right handed system, i.e. the
vector cross product of a unit vector along the positive x-axis and a
unit vector along the positive y-axis is equal to a unit vector along the
positive z-axis."
Some simple code to take one of the direction cosines (vectors) from the
Image Orientation (Patient) attribute and generate strings equivalent to
one of the values of Patient Orientation looks like this (noting that if
the vector is not aligned exactly with one of the major axes, the
resulting string will have multiple letters in as described under
"refinements" in C.7.6.1.1.1):
char * DerivedImagePlane::getOrientation(Vector3D vector) {
char *orientation=new char[4]; char *optr = orientation; *optr='\0';
char orientationX = vector.getX() < 0 ? 'R' : 'L'; char orientationY =
vector.getY() < 0 ? 'A' : 'P'; char orientationZ = vector.getZ() < 0 ?
'F' : 'H';
double absX = fabs(vector.getX()); double absY = fabs(vector.getY());
double absZ = fabs(vector.getZ());
int i; for (i=0; i<3; ++i) {
if (absX>.0001 && absX>absY && absX>absZ) {
*optr++=orientationX; absX=0;
} else if (absY>.0001 && absY>absX && absY>absZ) {
*optr++=orientationY; absY=0;
} else if (absZ>.0001 && absZ>absX && absZ>absY) {
*optr++=orientationZ; absZ=0;
} else break; *optr='\0';
} return orientation;
}
2.2.3 Determining the Transfer Syntax of DICOM input Streams
Another question that is frequently asked in comp.protocols.dicom is
how to read a DICOM dataset from, for example, a file, whether or not
there is a PS 3.10 style meta information header.
Firstly, if a DICOMDIR is being, it is always written with explicit VR
little endian transfer syntax, and a meta information header is always
present. Note also that DICOMDIRs are never sent over the network;
they are purely an interchange media object.
The meta information header is preceeded by a 128 byte preamble and
then the bytes 'DICM' as a magic number.
The meta-information that precedes the dataset of a PS 3.10 file is
always written in explicit VR little endian transfer syntax, and
contains within it tags which describe the succeeding dataset,
including what transfer syntax it is encoded in, something that needs
to be extracted and interpreted before proceeding to read past the end
of the meta information header and into the dataset. Note that the
group length of the meta information header elements is mandatory and
can be used to determine the end of the meta information header (i.e.,
when to change transfer syntaxes). Note that a draft of PS 3.10
before the final text suggested implicit VR for the meta-information
header, and some older applications may use that internally - these
non-DICOM files should never see the light of day however, and you can
probably forget about this.
The dataset following the meta information header will have the
specified transfer syntax, which obviously may be different from the
explicit VR little endian transfer syntax of the meta information
header itself. In the case of the most transfer syntaxes the encoding
of the data elements will subtly change at this point. In the case of
compressed pixel data transfer syntaxes everything will be the same as
the explicit VR little endian transfer syntax until one reaches
undefined length (7fe0,0010) elements. In the case of the deflated
compression transfer syntax, the defalted (zipped without the zip
header) bit stream will begin immediately after the last meta
information header attribute.
When one is unfortunate enough to encounter a file that has no
preamble and meta information header, then one has to guess the
transfer syntax, for example by assuming the object starts with low
group numbered tags and using the values of the first 16 bits to guess
big or little endian, and looking for upper case letters where an
explicit VR might be, and determining explicit or implicit VR from
that.
Note however, that there is no random intermingling of implicit and
explicit value representations. The transfer syntax dictates that
either one or the other is used throughout, after the meta information
header has been read.
Having said that, if you are reading something encoded in implicit VR,
then you can a) ignore the value by simply skipping it (using the VL
field), or b) interpret the value if you need to use it for something.
In the latter case you need to know in advance what the VR "should
be", i.e. you need a dictionary. However, that dictionary only needs
to be as long as the attributes you need to interpret ... all the
others can be skipped passively.
Note that it is NEVER necessary to test on the fly on a per-element
basis whether or not the value representation is implicit or explicit.
This is always decided before you start. Either you know the entire
dataset is explicit or implicit because you read the meta-information,
found the transfer syntax uid specified there and decided to switch to
that transfer syntax after the meta-information (the length of which
is always specified and tells you when to switch), or there was no
meta-information and you used some heuristic (or command line switch)
to decide what the transfer syntax is.
Here is one approach to handling the meta information header and guessing the
transfer syntax if none is present, written in C++, much as it is done in
dicom3tools:
void DicomInputStream::initializeTransferSyntax(const char *uid,bool meta) {
TransferSyntaxToReadMetaHeader = 0; TransferSyntaxToReadDataSet = 0; //
First make use of command line parameters that override guesswork ...
if (uid) {
TransferSyntax *ts = new TransferSyntax(uid); if (meta) {
TransferSyntaxToReadMetaHeader = ts; // specified UID is
transfer syntax to read metaheader
} else {
TransferSyntaxToReadDataSet = ts; // specified UID is
transfer syntax to read dataset (there is no metaheader)
}
} // else transfer syntax has to be determined by either guesswork or
metaheader ... char b[8]; if (meta) {
// test for metaheader prefix after 128 byte preamble
seekg(128,ios::beg); if (good() && read(b,4) &&
strncmp(b,"DICM",4) == 0) {
if (!TransferSyntaxToReadMetaHeader)
TransferSyntaxToReadMetaHeader = // guess only if not
specified on command line
read(b,6) && isupper(b[4]) && isupper(b[5]) ?
new
TransferSyntax(ExplicitVRLittleEndianTransferSyntaxUID)
// standard : new
TransferSyntax(ImplicitVRLittleEndianTransferSyntaxUID);
// old draft (e.g. used internally on GE IOS
platform)
// leaves positioned at start of metaheader
seekg(128+4,ios::beg);
} else {
clear(); seekg(0,ios::beg); // reset stream since
metaheader was sought but not found
TransferSyntaxToReadDataSet=TransferSyntaxToReadMetaHeader;
TransferSyntaxToReadMetaHeader=0;
}
} if (!TransferSyntaxToReadDataSet && !TransferSyntaxToReadMetaHeader) {
// was not specified on the command line and there is no metaheader
bool bigendian = false; bool explicitvr = false; clear();
seekg(0,ios::beg); if (good() && read(b,8)) {
// examine probable group number ... assume <= 0x00ff
if (b[0] < b[1]) bigendian=true; else if (b[0] == 0 &&
b[1] == 0) {
// blech ... group number is zero // no point
in looking at element number // as it will
probably be zero too (group length) // try the
32 bit value length of implicit vr if (b[4] <
b[7]) bigendian=true;
} // else littleendian if (isupper(b[4]) &&
isupper(b[5])) explicitvr=true;
} // else unrecognized ... assume default if (bigendian)
if (explicitvr)
TransferSyntaxToReadDataSet = new
TransferSyntax(ExplicitVRBigEndianTransferSyntaxUID);
else
TransferSyntaxToReadDataSet = new
TransferSyntax(ImplicitVR,BigEndian);
else
if (explicitvr)
TransferSyntaxToReadDataSet = new
TransferSyntax(ExplicitVRLittleEndianTransferSyntaxUID);
else
TransferSyntaxToReadDataSet = new
TransferSyntax(ImplicitVRLittleEndianTransferSyntaxUID);
// leaves positioned at start of dataset clear();
seekg(0,ios::beg);
} TransferSyntaxInUse = TransferSyntaxToReadMetaHeader ?
TransferSyntaxToReadMetaHeader : TransferSyntaxToReadDataSet;
Assert(TransferSyntaxInUse);
setEndian(TransferSyntaxInUse->getEndian());
}
Here is the same sort of thing in Java, paraphrasing the PixelMed Java DICOM
toolkit:
private void initializeTransferSyntax(String uid,boolean tryMeta) throws
IOException {
TransferSyntaxToReadMetaHeader = null; TransferSyntaxToReadDataSet =
null; byte b[] = new byte[8]; // First make use of argument that
overrides guesswork at transfer syntax ... if (uid != null) {
TransferSyntax ts = new TransferSyntax(uid); if (tryMeta) {
TransferSyntaxToReadMetaHeader = ts; // specified UID is
transfer syntax to read metaheader
} else {
TransferSyntaxToReadDataSet = ts; // specified UID is
transfer syntax to read dataset (there is no metaheader)
}
} // else transfer syntax has to be determined by either guesswork or
metaheader ... if (tryMeta) {
// test for metaheader prefix after 128 byte preamble if
(markSupported()) mark(140); if (skip(128) == 128 && read(b,0,4)
== 4 && new String(b,0,4).equals("DICM")) {
if (TransferSyntaxToReadMetaHeader == null) { // guess
only if not specified as an argument
if (markSupported()) {
mark(8); if (read(b,0,6) == 6) { // the
first 6 bytes of the first attribute tag
in the metaheader
TransferSyntaxToReadMetaHeader =
Character.isUpperCase((char)(b[4]))
&&
Character.isUpperCase((char)(b[5]))
? new
TransferSyntax(TransferSyntax.ExplicitVRLittleEndian)
// standard : new
TransferSyntax(TransferSyntax.ImplicitVRLittleEndian);
// old draft (e.g. used
internally on GE IOS
platform)
} else {
TransferSyntaxToReadMetaHeader =
new
TransferSyntax(TransferSyntax.ExplicitVRLittleEndian);
} reset();
} else {
// can't guess since can't rewind ...
insist on standard transfer syntax
TransferSyntaxToReadMetaHeader = new
TransferSyntax(TransferSyntax.ExplicitVRLittleEndian);
}
} byteOffsetOfStartOfData=132;
} else {
// no preamble, so rewind and try using the specified
transfer syntax (if any) for the dataset instead if
(markSupported()) {
reset(); TransferSyntaxToReadDataSet =
TransferSyntaxToReadMetaHeader; // may be null
anyway if no uid argument specified
byteOffsetOfStartOfData=0;
} else {
throw new IOException("Not a DICOM PS 3.10 file
- no DICM after preamble in metaheader, and
can't rewind input");
}
}
} // at this point either we have succeeded or failed at finding a
metaheader, or we didn't look // so we either have a detected or
specified transfer syntax for the metaheader, or the dataset, or nothing
at all if (TransferSyntaxToReadDataSet == null &&
TransferSyntaxToReadMetaHeader == null) { // was not specified as an
argument and there is no metaheader
boolean bigendian = false; boolean explicitvr = false; if
(markSupported()) {
mark(10); if (read(b,0,8) == 8) {
// examine probable group number ... assume <=
0x00ff if (b[0] < b[1]) bigendian=true; else if
(b[0] == 0 && b[1] == 0) {
// blech ... group number is zero // no
point in looking at element number // as
it will probably be zero too (group
length) // try the 32 bit value length
of implicit vr if (b[4] < b[7])
bigendian=true;
} // else little endian if
(Character.isUpperCase((char)(b[4])) &&
Character.isUpperCase((char)(b[5])))
explicitvr=true;
} // go back to start of dataset reset();
} // else can't guess or unrecognized ... assume default
ImplicitVRLittleEndian (most common without metaheader due to
Mallinckrodt CTN default) if (bigendian)
if (explicitvr)
TransferSyntaxToReadDataSet = new
TransferSyntax(TransferSyntax.ExplicitVRBigEndian);
else
throw new IOException("Not a DICOM file
(masquerades as explicit VR big endian)");
else
if (explicitvr)
TransferSyntaxToReadDataSet = new
TransferSyntax(TransferSyntax.ExplicitVRLittleEndian);
else
TransferSyntaxToReadDataSet = new
TransferSyntax(TransferSyntax.ImplicitVRLittleEndian);
}
TransferSyntaxInUse = TransferSyntaxToReadMetaHeader != null ?
TransferSyntaxToReadMetaHeader : TransferSyntaxToReadDataSet; if
(TransferSyntaxInUse == null) throw new IOException("Not a DICOM file
(or can't detect Transfer Syntax)");
setEndian(TransferSyntaxInUse.isBigEndian()); // leaves us positioned at
start of group and element tags (for either metaheader or dataset)
}
2.3 Papyrus
Papyrus is an image file format based on ACR/NEMA version 2.0. It was
developed by the Digital Imaging Unit of the University Hospital of
Geneva for the European project on telemedicine (TELEMED project of the
RACE program), under the leadership of Dr. Osman Ratib
(
[email protected]). The University Hospital of Geneva uses Papyrus
for their hospital-wide PACS.
The medical file format component of Papyrus version 2 extended the
ACR/NEMA format, particularly in order to reference multiple images by
placing folder information referencing ACR-NEMA data sets in a shadow
(private) group. Contributing to the development of DICOM 3, the team
are updating their format to be compatible with the offline file format
provisions of the draft Part 10 of DICOM 3 in Papyrus version 3.
The specifications, toolkit and image manipulation software that is
Papyrus aware, Osiris, is available for the Mac, Windows, and
Unix/X11/Motif by ftp from
ftp://expasy.hcuge.ch/pub/Osiris.
See also Papyrus and Osiris.
Further information is available in printed form. Contact
[email protected] (Yves Ligier).
2.4 Interfile V3.3
Interfile is a "file format for the exchange of nuclear medicine image
data" created I gather to satisfy the needs of the European COST B2
Project for the transfer of images of quality control phantoms, and
incorporates the AAPM (American Association of Physicists in Medicine)
Report No. 10, and has been subsequently used for clinical work.
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, see the Interfile sources,
Interfile information contacts and Interfile mailing list described
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
[email protected](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 from the Qsh ftp site. 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
ftp://sunsolve1.sun.com (192.9.9.24).
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
[email protected] (David Reddy) (see InterFormat
in the Sources section).
[Editorial note: this seems a bit of a shame to me - the old
distribution included lots of handy bits of information, particularly on
driving tape drives. I am advised however that the conversion stuff was
pulled out because people wanted it supported, the authors were worried
they were disclosing things perhaps they ought not to be, and NYU had
switched to using InterFormat themselves anyway. DAC.]
The authors of the qsh package are:
-
[email protected] (Gerald Q. (Chip) Maguire) -
[email protected] (Marilyn E Noz)
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=<noz88b>, Author=<M. E. Noz and G. Q. Maguire Jr.>,
Title=<QSH: A Minimal but Highly Portable Image Display
and Processing Toolkit>,
Journal=<Computer Methods and Programs in Biomedicine>,
volume=<27>, month=<November>, Year=<1988>, Pages=<229-240>
] @Article[maguire89e,
Key=<maguire>, Author=<G.Q. Maguire Jr., and M.E. Noz>,
Title=<Image Formats: Five Years after the AAPM Standard Format
for Digital Image Interchange>, Journal=<Medical Physics>,
volume=<16>, month=<September/October>, year=<1989>,
pages=<818-823>, comment=<Also as CUCS-369-88>
]
2.6 DEFF
DEFF (Data Exchange File Format) is a portable image file format
designed for the exchange, printing and archiving of ultrasound images.
It is written by John Bono of ATL from whom the specification may be
obtained. The latest version is 2.5, March 25, 1994. It is based on
the TIFF 5.0 specification, though a more recent version, TIFF 6.0 is
available.
Theorectically, any TIFF reader should be able to read the standard tags
from a DEFF image, so long as only 8 bit images are in use, as in the
Camera Ready class of DEFF images for instance. Additional support is
provided for multi-frame images, and 9 to 16 bit images by extending the
TIFF format. Because Aldus only allocates a small number of unique
registered tags to each vendor, ATL have defined their own extensive set
of additional tags, which are referenced by using one of the registered
tags ExtendedTagsOffset. Hence these additional tags will not be
visible to a conventional TIFF reader.
The next part is part3 - proprietary CT formats.
