medical image format faq - part 4.htm

mri_toolbox是一个工具用来MRI. 来自于SourceForge, 我上传这个软件,希望能结识对医疗软件感兴趣的兄弟.

        812       u_int      DOBMM                   
        816       u_int      DOBDD                   
        851       char[3]    PatientAge             
        854       char       PatientAgeUnits      ('Y'=years) 
        1052      u_int      RegistrationDateYYYY 
        1056      u_int      RegistrationDateMM 
        1060      u_int      RegistrationDateDD 
        1064      u_int      RegistrationTimeHH 
        1068      u_int      RegistrationTimeMM 
        1072      u_int      RegistrationTimeSS 
        1544      double     SliceThickness 
        1560      double     RepetitionTime
        1568      double     EchoTime
        1592      double     FrequencyMHz
        1639      char[5]    Station             
        1712      u_int      CalibrationDateYYYY 
        1716      u_int      CalibrationDateMM 
        1720      u_int      CalibrationDateDD 
        1724      u_int      CalibrationTimeHH 
        1728      u_int      CalibrationTimeMM 
        1732      u_int      CalibrationTimeSS 
        1767      char[16]   ReceivingCoil
        1828      char[4]    ImagedNucleus
        2112      double     FlipAngle
        2560      double     MagneticFieldStrength
        2864      u_int      DisplayMatrixSize 
        2944      char[65]   SequencePrgName
        3009      char[65]   SequenceWkcName 
        3074      char[9]    SequenceAuthor 
        3083      char[8]    SequenceType
        3744      double     FOVRow             
        3752      double     FOVColumn             
        3768      double     CenterPointX             
        3776      double     CenterPointY             
        3784      double     CenterPointZ             
        3792      double     NormalVectorX             
        3800      double     NormalVectorY             
        3808      double     NormalVectorZ             
        3816      double     DistanceFromIsocenter 
        3832      double     RowVectorX             
        3840      double     RowVectorY             
        3848      double     RowVectorZ             
        3856      double     ColumnVectorX             
        3864      double     ColumnVectorY             
        3872      double     ColumnVectorZ             
        3880      char[3]    OrientationSet1Top 
        3884      char[3]    OrientationSet1Left 
        3888      char[3]    OrientationSet1Back 
        3892      char[3]    OrientationSet2Down 
        3896      char[3]    OrientationSet2Right 
        3900      char[3]    OrientationSet2Front 
        3904      char[32]   SequenceName             
        5000      double     PixelSizeRow             
        5008      double     PixelSizeColumn 

        5504      char[12]   TextPatientID             
        5517      char       TextPatientSex 
        5518      char[3]    TextPatientAge 
        5521      char       TextPatientAgeUnits       ('Y'=years) 
        5529      char[7]    TextPatientPosition 
        5541      char[5]    TextImageNumberFlag       ('IMAGE'=image) 
        5546      char[3]    TextImageNumber
        5559      char[2]    TextDateDD             
        5562      char[3]    TextDateMM             
        5566      char[4]    TextDateYYYY             
        5571      char[2]    TextTimeHH             
        5574      char[2]    TextTimeMM             
        5577      char[2]    TextAcquisitionTimeFlag   ('TA'=acquisition time) 
        5583      char[2]    TextAcquisitionTimeMM             
        5586      char[2]    TextAcquisitionTimeSS             
        5601      char[4]    TextAnnotation
        5655      char[25]   TextOrganization             
        5682      char[5]    TextStation                   
        5695      char[3]    TextAcquisitionMatrixPhase
        5698      char       TextAcquisitionMatrixPhaseAxis  ('h'=horizontal,' '=vertical) 
        5700      char[3]    TextAcquisitionMatrixFreq 
        5703      char       TextAcquisitionMatrixFreqO      ('o'=o,' '=blank) 
        5704      char       TextAcquisitionMatrixFreqS      ('s'=s,' '=blank) 
        5706      char[8]    TextSequence                   
        5714      char[3]    TextFlipAngle                   
        5718      char[4]    TextScanNumberFlag        ('SCAN'=scan) 
        5723      char[3]    TextScanNumberA             
        5726      char[3]    TextScanNumberB             
        5730      char[2]    TextRepetitionTimeFlag    ('TR'=tr) 
        5734      char[7]    TextRepetitionTime             
        5742      char[2]    TextEchoTimeFlag          ('TE'=te) 
        5746      char[5]    TextEchoTime                   
        5752      char       TextEchoNumber             
        5790      char[2]    TextSliceThicknessFlag    ('SL'=slice thickness) 
        5794      char[7]    TextSliceThickness
        5802      char[2]    TextSlicePositionFlag     ('SP'=slice position) 
        5806      char[7]    TextSlicePosition
        5814      char[3]    TextAngleFlag1            ('Sag'=sagittal,'Cor'=coronal,'Tra'=transverse) 
        5817      char       TextAngleFlag2            ('>'=gt,'<'=lt) 
        5818      char[3]    TextAngleFlag3            ('Sag'=sagittal,'Cor'=coronal,'Tra'=transverse) 
        5821      char[4]    TextAngle                   
        5838      char[3]    TextFOVFlag               ('FoV'=field of view) 
        5842      char[3]    TextFOVH                   
        5846      char[3]    TextFOVV                   
        5874      char[2]    TextTablePositionFlag     ('TP'=table position) 
        5878      char[7]    TextTablePosition             
        5938      char[5]    TextStudyNumberFlag       ('STUDY'=study) 
        5943      char[2]    TextStudyNumber
        5956      char[2]    TextDOBDD                   
        5959      char[3]    TextDOBMM                   
        5963      char[4]    TextDOBYYYY                   
        5992      char[3]    TextStudyNumberFlag2      ('STU'=study) 
        5996      char[3]    TextImageNumberFlag2      ('IMA'=study) 
        5999      char[2]    TextStudyNumber2             
        6002      char[2]    TextImageNumber2             
        6013      char[5]    TextStudyImageNumber3             
        6031      char[15]   TextModelName                   
        6058      char[25]   TextPatientName             
        6085      char[2]    TextScanStartTimeHH             
        6088      char[2]    TextScanStartTimeMM             
        6091      char[2]    TextScanStartTimeSS             
</PRE>
<H6>3.3.2.4.2 <A name=MagnetomVisionSPI>Siemens Magnetom Vision SPI 
Format</A></H6>
<P>Unknown. </P>
<H4>3.3.3 <A name=MRPhilips>Philips MR</A></H4>
<H5>3.3.3.1 <A name=PhilipsS5>Philips Gyroscan S5</A></H5>
<UL>
  <LI>can export as ACR/NEMA (actually SPI) files 
  <LI>little endian byte order 
  <LI>12 bit packed data </LI></UL>
<P>This description pertains to "exported ACR/NEMA", not the native image files, 
which I am not familiar with. In fact I am not even sure in which directory they 
live. </P>
<P>Use the ADMIN menu on the operator's console to find the import/export 
ACR/NEMA utility, with which you can select an exam, series or image to export 
as an ACR/NEMA file. The default directory is the GYROVIEW home directory, which 
is already pretty cluttered so it is better to make another subdirectory like 
"ANI" to keep exported files in. The exported files have huge names composed of 
identification information, but all have a ".ANI" extension. For example: </P><PRE>        DIR SYS$SYSROOT:[GYROSCAN]*.ANI;*

        SMITH__FA02010801010001.ANI;1
</PRE>
<P>These files are stored as, wait for it, fixed length 512 byte records, with 
the "carriage return carriage control" record attributes set from some bizarre 
reason, which totally messes up kermit which starts messing with adding and 
changing CR/LF characters. See the Vax diatribe below for a method of getting 
around this, by using DUMP as a poor man's uuencode permitting ascii transfer. 
Unfortunately the nature of fixed length records under VMS means that the last 
record will be padded out to 512 bytes without any indication of the "real" 
end-of-file. This means your ACR/NEMA reader has to cope with trailing garbage 
gracefully. </P>
<P>Unlike the Siemens SPI files, the Philips ones are stored in little-endian 
format. There is no fixed size header to skip, just go straight into the 
ACR/NEMA data stream. For the image pixel data four 12 bit words are packed 
without padding into 16 bit words, without any compression sheme. See the 
ACR/NEMA section for description of the packing organization. Lots of private 
tags are defined, but these can be ignored. Some of the identifying tags present 
are as follows: </P><PRE>(0000x8,000x10) CS RecognitionCode       VR=&lt;CS&gt;   VL=&lt;0xc&gt;  &lt;ACR-NEMA 1.0&gt; 
(0000x8,000x70) LO Manufacturer          VR=&lt;LO&gt;   VL=&lt;0x8&gt;  &lt;Philips &gt; 
(0000x8,0x1090) LO ManufacturerModelName VR=&lt;LO&gt;   VL=&lt;0x2&gt;  &lt;S5&gt; 
(0000x9,000x10) LT SPIComments   VR=&lt;LT&gt;   VL=&lt;0xe&gt;   &lt;SPI Release 1 &gt; 
(000x19,000x10)                  VR=&lt;LT&gt;   VL=&lt;0x14&gt;  &lt;PHILIPS MR R5.6/PART&gt; 
</PRE>
<P>To get the files off, I plug a portable with a serial cable into one of the 
spare serial ports inside one of the Vax cabinets, at 9600 baud, and login as 
"GYROVIEW/NOCOM" without any password needed. This dumps you in the same 
directory as the files will be stored by default. You will probably need to set 
local echo on on your portable, or "SET TERMINAL/ECHO" on the Vax. Kermit was 
already loaded on my system, accessed as "RUN [SYSEXE]KERMIT". See the Vax 
section later for more help. </P>
<H5>3.3.3.2 <A name=#PhilipsMRACS>Philips Gyroscan ACS</A></H5>
<H5>3.3.3.3 <A name=PhilipsT5>Philips Gyroscan T5</A></H5>
<H5>3.3.3.4 <A name=PhilipsNT>Philips Gyroscan NT5 &amp; NT15</A></H5>
<H4>3.3.4 <A name=MRPicker>Picker MR</A> - another black hole</H4>
<H4>3.3.5 <A name=MRToshiba>Toshiba MR</A> - another black hole</H4>
<H4>3.3.6 <A name=MRHitachi>Hitachi MR</A> - another black hole</H4>
<H4>3.3.7 <A name=MRShimadzu>Shimadzu MR</A></H4>
<P>The following information pertains to Revision 3 of the Shimadzu MRI format. 
The new Revision 4 doesn't change this apparently. </P>
<UL>
  <LI>words are big endian 
  <LI>fixed layout header 
  <UL>
    <LI>standard 512 bytes 
    <LI>extended 2048 bytes (1st 512 same) 
    <LI>extended indicated by high byte of ZHREV non-zero </LI></UL>
  <LI>16 bit uncompressed image pixel data 
  <LI>starting block of image pixel data is ZIBLKA (from 1) 
  <LI>multiple images per file, number specified in ZIMAGE 
  <LI>offset to image pixel data specified by index after header 
  <UL>
    <LI>each index entry is 48 bytes for standard 
    <LI>each index entry is 256 bytes for extended 
    <LI>starting block for image added to ZIBLKA is 
    <UL>
      <LI>int16 at byte 30 (from 0) of entry (standard) 
      <LI>int16 at byte 50 + (int16 at byte 52 &lt;&lt; 16) (extended)<BR>(NB. 
      Not the same at big-endian int32 at byte 50) </LI></UL></LI></UL>
  <LI>physical location of each slice is encoded in 
  <UL>
    <LI>ZSLOC slice Location 
    <LI>ZSLOC int16 at byte offset 8 (from 0) of index entry 
    <LI>ZSLOC is relative to isocenter (same units as ZCLOC) </LI></UL>
  <LI>elapsed time of each slice is encoded in 
  <UL>
    <LI>ZPTIM1 int16 at byte offset 6 (from 0) of index entry 
    <LI>ZPTIM1 units are seconds since first slice </LI></UL>
  <LI>field of view 
  <UL>
    <LI>ZVIEW give the real field of view in mm*10 units 
    <LI>better than the mnemonic code in the ZAAREA field </LI></UL></LI></UL>
<P>The following information pertains to Revision 3 of the Shimadzu MRI format. 
The new Revision 4 doesn't change this apparently. The offsets are specified in 
both bytes from 0 and words from 1 (the Shimadzu convention). </P><PRE>	Standard Header or 1st 512 bytes of Extended Header:

	Offset	Offset	Type	Keyword	Description	Units	Example
	(Bytes)	(Words)

	0	1	char 8	ZASYSID	SYS-ID
	8	5	char 16	ZANAME	NAME
	24	13	char 12	ZAID	ID
	36	19	char 2	ZASEX	SEX			"M ","F "
	38	20	char 4	ZAAGE	AGE		years
	42	22	char 20	ZACOMM	COMMENT
	62	32	char 18	ZAHOSP	HOSPITAL
	80	41	char 8	ZADATW	DATE			"YY-MM-DD"
	88	45	char 8	ZATIME	TIME			"HH:MM:SS"
	96	49	char 8	ZAAREA	Zoom Size/NSlices	"1.0 S/10"
						ES = 100mm
						VS = 150mm
						SS = 200mm
						 S = 250mm
						 M = 300mm
						 L = 350mm
						LL = 400mm
	104	53	char 8	ZASEQ	TYPE/MODE		"IR/256" where 256 is Max(Nx,Ny)
						IR = Inversion Recovery
						SE = Spin Echo
						FE = Field Echo
	112	57	char 8	ZATR	TR		mS	"TR=1500"
	120	61	char 8	ZATE	TE		mS	"TE=150"
	128	65	char 8	ZATI	TI		mS	"TI=200"
	136	69	char 8	ZALOK	LOCATION	M