📄 medical image format faq - part 4.htm
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<H1><IMG src="Medical Image Format FAQ - Part 4_files/title.gif"> Medical Image
Format FAQ - Part 4</H1>
<HR>
<H1>Proprietary Formats (Continued)</H1>
<HR>
<H2>Access to other parts ...</H2>
<UL>
<LI><A
href="http://www.dclunie.com/medical-image-faq/html/index.html">preface</A>
<LI><A
href="http://www.dclunie.com/medical-image-faq/html/changes.html">latest
changes</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/toc.html">table of
contents</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part1.html">part1 -
general information & standard formats</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part2.html">part2 -
standard formats (continued)</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part3.html">part3 -
proprietary CT formats</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part4.html">part4 -
proprietary MR formats</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part5.html">part5 -
proprietary other formats</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part6.html">part6 -
hosts & compression</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part7.html">part7 -
general information sources</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/part8.html">part8 -
DICOM information sources</A>
<LI><A href="http://www.dclunie.com/medical-image-faq/html/keyword.html">index
by keyword</A> </LI></UL><BR>START OF PART 4<BR>
<H3>3.3 <A name=ProprietaryMR>MR - Proprietary Formats</A></H3>
<H4>3.3.1 <A name=MRGE>General Electric MR</A></H4>
<H5>3.3.1.1 <A name=Signa3X4X>GE MR Signa 3.x,4.x</A></H5>
<P>References (see the <A
href="http://www.dclunie.com/medical-image-faq/html/part7.html#GEContactFormats">GEMS
image format information contacts</A> section): </P>
<UL>
<LI>46-021858 MR Signa 4.x Mag Tape/Image Fmt <BR></LI></UL>
<H6>3.3.1.1.1 <A name=Signa3X4XImage>GE MR Signa 3.x,4.x Image data</A></H6>
<UL>
<LI>"fixed format" header
<LI>image data is not compressed
<LI>image data fixed offset 14336 bytes
<LI>Data General host
<LI>AOS/VS </LI></UL>
<P>The image files are of fixed layout, described here as a series of 256 by 16
bit word blocks (512 bytes), blocks numbered from 0. The headers start at the
following block offsets: </P><PRE> block 0 - length 4 blocks - System configuration
block 4 - length 2 blocks - Site customization
block 6 - length 2 blocks - Study header
block 8 - length 2 blocks - Series header
block 10 - length 2 blocks - Image header
block 12 - length 4 blocks - Raw database header
block 16 - length 10 blocks - Pulse sequence description
block 26 - length 2 blocks - Pixel map (? not ever used)
block 28 - length 256 blocks - Image data
</PRE>
<P>As decribed earlier, the header is a fixed length of 14336 bytes, after which
the uncompressed image data starts. </P>
<P>Some of the more important fields are described here. Integers are 16 bit
words (big-endian), ascii strings are Fortran style specifications with length
in bytes, and reals are 4 bytes long (see Host machines - Data General), word
offsets are numbered from 0: </P><PRE> block 6 - study header
word 32 - 5A - Study number
word 39 - 9A - Date of study (dd-mmm-yy)
word 47 - 8A - Time of study (hh:mm:ss)
word 54 - 32A - Patient name
word 70 - 12A - Patient ID
word 78 - 3A - Age xxx years or xxD or W or M or Y
word 80 - 1A - Sex
block 8 - series header
word 31 - 3A - Series number
word 52 - 120A - Series description
word 112 - Int - Series type (0=normal,1=screensave,
2=composite)
word 113 - Int - Coil type (0=head,1=body,2=surface)
word 114 - 16A - Coil name
word 122 - Int - Contrast description
word 138 - Int - Plane type (0=axial,1=sagittal,2=coronal,
3=oblique,4=screen save)
word 147 - Int - Image mode (0=2D single,1=2D multiple,
2=3D volume,3=cine,4=spectroscopy)
word 148 - Int - Field strength (gauss)
word 149 - Int - Pulse sequence (0=memp,1=ir,2=ps,3=rm,
4=rmge,5=gre,6=vemp,7=mpgr,8=mpgrv,
9=mpirs,10=mpiri,11=3d/gre,
12=cine/gre,13=spgr,14=sspf,
15=cin/spgr,16=3d/spgr,17=fse,
18=fve,19=fspgr,20=fgr,21=fmpspgr,
22=fmpgr,23=fmpir,24=probe.s,
25=probe.p)
word 150 - Int - Pulse sequence subtype (0=chopper)
word 151 - Real - Field of view mm
word 153 - Real - Center (3 values;R+L-,A+P-,S+I-)
word 159 - Int - Orientation (0=supine,1=prone,2=Lt,3=Rt)
word 160 - Int - Position (0=head first,1=feet first)
word 161 - 32A - Longitudinal anatomical reference
word 177 - 32A - Vertical anatomical reference
word 199 - Int - Scan matrix X
word 200 - Int - Scan matrix Y
word 201 - Int - Image matrix
block 10 - image header
word 44 - 3A - Image number
word 73 - Real - Image location
word 75 - Real - Table position
word 77 - Real - Image thickness
word 79 - Real - Image spacing
word 82 - Real - TR uS
word 86 - Real - TE uS
word 88 - Real - TI uS
word 98 - Int - Number of echos
word 99 - Int - Echo number
word 101 - Int - NEX (if not fractional)
word 146 - Real - NEX
word 175 - Int - Flip angle
</PRE>
<H6>3.3.1.1.2 <A name=Signa3X4XTape>GE MR Signa 3.x,4.x Tape format</A></H6>
<H6>3.3.1.1.3 <A name=Signa3X4XRaw>GE MR Signa 3.x,4.x Raw data</A></H6>
<H5>3.3.1.2 <A name=Signa5X>GE MR Signa 5.x - Genesis</A></H5>
<P>References (see the <A
href="http://www.dclunie.com/medical-image-faq/html/part7.html#GEContactFormats">GEMS
image format information contacts</A> section): </P>
<UL>
<LI>46-021861 Image Data Format <BR>
<LI>46-021863 Optical Disk Raw Partition <BR>
<LI>46-021864 Image Extract Tool <BR>
<LI>46-021865 DAT Archive Format <BR></LI></UL>
<P>General Electric now uses the same Sun based architecture for its HighLite
Advantage (HLA) and High Speed Advantage (HSA) CT and Signa 5X MR family,
referred to as Genesis. The general details of this scheme will be discussed
here, as well as the description of the MR image header. Specifics related to
the CT modality are described elsewhere. </P>
<H6>3.3.1.2.1 <A name=Signa5XImage>GE MR Signa 5.x Image data</A></H6>
<P>Genesis is a system running under SunOS 3.5G (NOT Solaris) on, believe it or
not, a sun3 68000 architecture, not a sun4 sparc. </P>
<P>It would appear that unlike in the previous Data General based system, the
active database is stored as one large monolithic file in a raw partition, which
doesn't make it very easy to extract single imgaes. Fortunately, GE have saved
the day by kindly providing, and thoroughly documenting in the material that
they send you when you ask for the image file format, an Image Extract Tool that
lives in "/usr/g/insite/bin" and is called "ximg". To see what options are
available just type "ximg -h" for help. Note that ximg's default is to strip out
the patient's name and ID number which is annoying, so don't forget the "-s"
flag. The default directory to put the extracted images in is
"/usr/g/insite/tmp". The input names to select images in silent (non-menu) mode
are of the following form: </P><PRE> EeeeeeSsssIiii
eeeee = exam number or "all"
sss = series number or "all"
iii = image number or "all"
</PRE>
<P>and the resultant filenames are the same with an extension of ".MR" or ".CT"
depending. For example: </P><PRE> % /usr/g/insite/bin/ximg -i e673s1i1 -s -t
% ls -l /usr/g/insite/tmp
E673S1I1.MR
</PRE>
<P>which extracts the selected image in silent mode (-i) without stripping the
identification (-s) in rectangular (-t) mode, ie. not compressed or packed. </P>
<P>One nifty feature that allows you to keep up to date with the latest version
header contents is the "-g" switch which invokes the GenIncl utility that
produces a file called "imageFileOffsets.h" that lists the type and offsets of
each field in the header ! Remarkable, huh ? </P>
<P>How does one get access to the operating system on the Signa ? Let me count
the ways. First, from the Advantage console one can just call up a command shell
from the Utilities menu, or one can invoke the Ftp option uner Networks and then
use the "!" command to ftp, which like in many Unix tools, spawns a shell. Or
from another workstation on the network one can just telnet or rsh across. If
you are connected using an Advantage Windows workstation you can pull up a
command shell by using the right menu button with the cursor on the desktop.
Doing a few "cat /etc/hosts" around the place will let you know what all the
machines are called. </P>
<P>One can also access the console directly from the plasma screen by toggling
"L1-B" on or off. </P>
<P>Once you have extracted them, the Genesis file contains headers consisting of
several components in common with CT and then a specific CT or MR header. The
file is structured as a "block type" header with a brief "control header" of
fixed size, followed by a bunch of optional headers, some of which reflect
internal database structures and are of no interest, others (such as the
suite/exam/series/image) headers that contain descriptive and identification
information, and two that are of importance for deciphering the pixel data
(unpack control & compression control). Some of the more important fields
are described here: </P>
<P>Sun3 <A
href="http://www.dclunie.com/medical-image-faq/html/part6.html#SunData">Sun
Data</A> Types:
<UL>
<LI>short is 16 bits
<LI>int is 32 bits
<LI>float is 32 bits IEEE
<LI>double is 64 bits IEEE
<LI>byte offsets from 0 start of file
<LI>length ==0 means header absent/empty </LI></UL>
<P></P><PRE> control header (offset 0):
0 - int - magic number = 0x494d4746 = "IMGF"
4 - int - byte displacement to pixel data
8 - int - width
12 - int - height
16 - int - depth (bits)
20 - int - compression (0=asis,1=rectangular,2=packed,
3=compressed,4=compressed&packed)
32 - int - background shade to use for non-image
54 - u_short - 16 bit end_around_carry sum of pixels
56 - int - ptr to unique image identifier
60 - int - length of unique image identifier
64 - int - ptr to unpack header
68 - int - length of unpack header
72 - int - ptr to compression header
76 - int - length of compression header
80 - int - ptr to histogram header
84 - int - length of histogram header
88 - int - ptr to text plane
92 - int - length of text plane
96 - int - ptr to graphics plane
100 - int - length of graphics plane
104 - int - ptr to data base header
108 - int - length of data base header
112 - int - value to add to stored pixels
116 - int - ptr to user defined data
120 - int - length of user defined data
124 - int - ptr to suite header
128 - int - length of suite header
132 - int - ptr to exam header
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