Hi Frank, Are you using GDCM-2? This would explain the different messages from 3M3 and your compiled application. We have not had the chance yet to ensure GDCM2-compatibility of the diffusion module. Could you try using the old GDCM?
Best regards Klaus -----Ursprüngliche Nachricht----- Von: Frank Blaschke [mailto:[email protected]] Gesendet: Donnerstag, 15. Juli 2010 10:15 An: Fritzsche Klaus Cc: [email protected] Betreff: [mitk-users] MITK ExtApp Diffusion-Plugin Hi, now we tried to import our DICOM datasets with 3M3 application and import works. When i do it with ExtApp on windows i get an error message: WARNING: In C:\src\InsightToolkit\Code\IO\itkGDCMSeriesFileNames.cxx, GDCMSeriesFilenames (0xdbf66338): C:/workspace/Datensaetze/Datensatz... WARNING: In C:\src\InsightToolkit\Code\IO\itkGDCMSeriesFileNames.cxx, GDCMSeriesFilenames (0xdbf66338): No Series were found So I'm confused between the different errors on windows and linux with the same datasets and application. 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
