Hi Klaus, we've looked again in the DICOM files. In tag <0029,1010> are B_value and DiffusionGradientDirection values. Bevore we used ImageJ to get image informations, now with DicomToolkit there was more informations readable.
Here is an Hexdump from header [...] 00000d40h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000d50h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000d60h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000d70h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000d80h: 42 5F 76 61 6C 75 65 00 65 6E 73 61 74 69 6F 6E ; B_value.ensation 00000d90h: 50 38 59 07 50 38 59 07 6C 69 74 75 64 65 5B 32 ; P8Y.P8Y.litude[2 00000da0h: 60 38 59 07 60 38 59 07 32 32 34 35 35 37 0A 73 ; `8Y.`8Y.224557.s 00000db0h: 70 38 59 07 70 38 59 07 2E 73 45 64 64 79 43 6F ; p8Y.p8Y..sEddyCo 00000dc0h: 01 00 00 00 49 53 00 00 06 00 00 00 06 00 00 00 ; ....IS.......... 00000dd0h: 4D 00 00 00 09 00 00 00 09 00 00 00 4D 00 00 00 ; M...........M... 00000de0h: 09 00 00 00 31 30 30 30 20 20 20 20 00 00 00 00 ; ....1000 .... 00000df0h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000e00h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00000e10h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... (maybe b value is 1000?) [...] 00001630h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00001640h: 00 00 00 00 00 00 00 00 CD 00 00 00 00 00 00 00 ; ........Í....... 00001650h: 4E 75 6D 62 65 72 4F 66 49 6D 61 67 65 73 49 6E ; NumberOfImagesIn 00001660h: 4D 6F 73 61 69 63 00 07 66 6C 4B 44 79 6E 4D 61 ; Mosaic..flKDynMa 00001670h: C0 4A 59 07 C0 4A 59 07 69 6E 20 20 20 20 20 20 ; ÀJY.ÀJY.in 00001680h: D0 4A 59 07 D0 4A 59 07 20 3D 20 30 2E 35 0A 73 ; ÐJY.ÐJY. = 0.5.s 00001690h: 01 00 00 00 55 53 00 00 0A 00 00 00 00 00 00 00 ; ....US.......... 000016a0h: CD 00 00 00 44 69 66 66 75 73 69 6F 6E 47 72 61 ; Í...DiffusionGra 000016b0h: 64 69 65 6E 74 44 69 72 65 63 74 69 6F 6E 00 75 ; dientDirection.u 000016c0h: 63 52 46 50 10 4C 59 07 10 4C 59 07 20 20 20 20 ; cRFP.LY..LY. 000016d0h: 20 20 20 20 20 4C 59 07 20 4C 59 07 20 20 20 20 ; LY. LY. 000016e0h: 3D 20 30 78 03 00 00 00 46 44 00 00 04 00 00 00 ; = 0x....FD...... 000016f0h: 06 00 00 00 4D 00 00 00 0B 00 00 00 0B 00 00 00 ; ....M........... 00001700h: 4D 00 00 00 0B 00 00 00 30 2E 30 30 30 30 30 30 ; M.......0.000000 00001710h: 30 30 00 00 0B 00 00 00 0B 00 00 00 4D 00 00 00 ; 00..........M... 00001720h: 0B 00 00 00 30 2E 30 30 30 30 30 30 30 30 00 00 ; ....0.00000000.. 00001730h: 0B 00 00 00 0B 00 00 00 4D 00 00 00 0B 00 00 00 ; ........M....... 00001740h: 30 2E 30 30 30 30 30 30 30 30 00 00 00 00 00 00 ; 0.00000000...... 00001750h: 00 00 00 00 CD 00 00 00 00 00 00 00 00 00 00 00 ; ....Í........... 00001760h: 00 00 00 00 CD 00 00 00 00 00 00 00 00 00 00 00 ; ....Í........... (maybe gradientDirection is 0 0 0 ?) best regards Frank > Tue, 13 Jul 2010 12:20:11 +0200 - Fritzsche Klaus > <[email protected]>: > AW: AW: [mitk-users] MITK ExtApp Diffusion-Plugin > Hi Frank, > > I parsed one of my diffusion-files and it looks like this: > > Private_0029_1008: 'IMAGE NUM 4' > Private_0029_1009: '20090122' > Private_0029_1010: [10023x1 uint8] > Private_0029_1018: 'MR' > Private_0029_1019: '20090122' > Private_0029_1020: [80111x1 uint8] > Private_0029_1160: 'com' > > and "0029_1010" contains the following keywords: > > EchoLinePosition, EchoColumnPosition, EchoPartitionPosition, > UsedChannelMask, Actual3DImaPartNumber, ICE_Dims, B_value, Filter1, > Filter2, ProtocolSliceNumber, RealDwellTime, PixelFile, > PixelFileName, SliceMeasurementDuration, SequenceMask, > AcquisitionMatrixText, MeasuredFourierLines, FlowEncodingDirection, > FlowVenc, PhaseEncodingDirectionPositive, NumberOfImagesInMosaic, > DiffusionGradientDirection, ImageGroup, SliceNormalVector, > DiffusionDirectionality, TimeAfterStart, FlipAngle, SequenceName, > RepetitionTime, EchoTime, NumberOfAverages, VoxelThickness, > VoxelPhaseFOV, VoxelReadoutFOV, VoxelPositionSag, VoxelPositionCor, > VoxelPositionTra, VoxelNormalSag, VoxelNormalCor, VoxelNormalTra, > VoxelInPlaneRot, ImagePositionPatient, ImageOrientationPatient, > PixelSpacing, SliceLocation, SliceThickness, > SpectrumTextRegionLabel, Comp_Algorithm, Comp_Blended, > Comp_ManualAdjusted, Comp_AutoParam, Comp_AdjustedParam, Comp_JobID, > FMRIStimulInfo, FlowEncodingDirectionString, > RepetitionTimeEffective, CsiImagePositionPatient, > CsiImageOrientationPatient, CsiPixelSpacing, CsiSliceLocation, > CsiSliceThickness, OriginalSeriesNumber, OriginalImageNumber, > ImaAbsTablePosition, NonPlanarImage, MoCoQMeasure, LQAlgorithm, > SlicePosition_PCS, RBMoCoTrans, RBMoCoRot, MultistepIndex, > ImaRelTablePosition, ImaCoilString, RFSWDDataType, GSWDDataType, > NormalizeManipulated, ImaPATModeText, B_matrix, > BandwidthPerPixelPhaseEncode, FMRIStimulLevel, MosaicRefAcqTimes, > AutoInlineImageFilterEnabled > > Only "DiffusionGradientDirection" and "B_value" are used. > > Could you identify other TAGS in your dataset that exhibit the > b-value and gradient information? Do you know of different > conventions between different SIEMENS scanners? > > Best regards > Klaus Fritzsche > > > ________________________________________ > Von: Frank Blaschke [[email protected]] > Gesendet: Dienstag, 13. Juli 2010 11:14 > An: Fritzsche Klaus > Cc: [email protected] > Betreff: Re: AW: [mitk-users] MITK ExtApp Diffusion-Plugin > > Hi, > > we use the standart SIEMENS DWI product sequence. We've looked in our > DICOM tags: > > 0029,0010 ---: SIEMENS CSA HEADER > 0029,0011 ---: SIEMENS MEDCOM HEADER > 0029,0012 ---: SIEMENS MEDCOM HEADER2 > 0029,1008 ---: IMAGE NUM 4 > 0029,1009 ---: 20100209 > 0029,1018 ---: MR > 0029,1019 ---: 20100209 > 0029,1131 ---: 4.0.386076244 > 0029,1134 ---: DB TO DICOM > 0029,1260 ---: com > > What has to stand in there? > > best regards > > Frank > > >> the DICOM import has been tested on SIEMENS-datasets, but it looks >> like it is not able to find the correct meta-information in your >> datasets. >> >> The code in >> >> >> Modules/DiffusionImaging/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp >> >> checks the private DICOM-tag "0029,1010", do you have a chance to >> take a look at the tag in your datasets? > > > > > > > >> >> Hi, >> >> i wanna use the mitk.gui.qt.diffusionimagin plugin. It include DICOM >> Import extension. When I try to use it, i get the following console >> output: >> >> s...@judika:~$ /usr/lib/mitk/bin/ExtApp >> [Mon Jul 12 14:02:09 2010 >> 0.110] Registering CoreExtObjectFactory... >> [0.110] CoreObjectFactory c'tor >> [0.110] CoreExtObjectFactory c'tor >> [0.110] CoreObjectFactory: registering extra factory of type >> CoreExtObjectFactory >> [0.260] Registering DiffusionImagingObjectFactory... >> [0.260] DiffusionImagingObjectFactory c'tor >> [0.260] CoreObjectFactory: registering extra factory of type >> DiffusionImagingObjectFactory >> [0.260] CoreObjectFactory: registering extra factory of type >> DiffusionImagingObjectFactory >> [0.270] Registering PlanarFigureObjectFactory... >> [0.270] PlanarFigureObjectFactory c'tor >> [0.270] CoreObjectFactory: registering extra factory of type >> PlanarFigureObjectFactory >> [0.330] QmitkRegisterClasses() >> [0.340] QmitkExtRegisterClasses() >> [0.950] [BlueBerry] BlueBerry Workbench ready >> >> Image #1/1 Dims 512x512x3 Warning: No B_value in >> /home/salz/workspace/MRT-Datensaetze/Data01/MR.1.3.12.2.1107.5.2.13.20566.30000010020907204484300004401 >> Probe Tag Starts Stops Time (s) >> Directory Parsing 1 1 0.018 >> Header Reading 1 1 0.119 >> Volume Loading 1 0 0.000 >> Aborted >> s...@judika:~$ >> >> Every other files i tried to use ExtApp crashes. Are there special >> requirements for DICOM files to use them with Diffusion-Plugin? The >> normal way to import them in ExtApp works. >> >> I use Ubuntu 9.10 >> gcc-4.4.1 >> CMake-2.8.0 >> VTK-5.6.0 >> ITK-3.18.0 >> Qt-4.5.3 >> MITK-svn-2010-07-12 (#24511) >> boost-1.43.0 >> >> Greetings >> >> Frank >> > -- Frank Blaschke Department for Biometry and Medical Informatics web: http://www.med.uni-magdeburg.de/ibmi.html phone: +49 391 67 135 51 office: building 2 / room 212 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
