I'm new to processing DICOM images away from their native manufacturer software. I am trying to dicomread a PET image from a set of reconstructed transaxial slices into MatLab. My aim is to do some simple segmentation and finally determine the maximum and minimum pixel value in the segment. However I am having trouble with converting the stored values to their values seen on the native system.
The image is loading into MatLab as an int16 class. The maximum pixel value is always 32767, regardless of which slice I load from the series. I know from viewing the images on their native system that the maximum pixel value in each slice is different.
I've checked the rescale value and rescale intercept values and the rescale relationship appears to be linear. Is there another correction I should be making? I assume all other corrections (e.g. decay, scatter and randoms) are made during the reconstruction process.
Any help would be appreciated (hopefully I'm missing something simple!).I've posted the DICOM info retrieved from the header below (Don't worry, the images are of a phantom so there is no patient identifying data).
Regards,
Ross
Filename: [1x76 char]
FileModDate: '26-Jul-2013 10:50:42'
FileSize: 38356
Format: 'DICOM'
FormatVersion: 3
Width: 128
Height: 128
BitDepth: 16
ColorType: 'grayscale'
FileMetaInformationGroupLength: 182
FileMetaInformationVersion: [2x1 uint8]
MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.128'
MediaStorageSOPInstanceUID: [1x49 char]
TransferSyntaxUID: '1.2.840.10008.1.2.1'
ImplementationClassUID: '1.2.840.113619.6.55'
SourceApplicationEntityTitle: 'dst01'
IdentifyingGroupLength: 484
SpecificCharacterSet: 'ISO_IR 100'
ImageType: 'ORIGINAL\PRIMARY'
InstanceCreationDate: '20130522'
InstanceCreationTime: '171655'
InstanceCreatorUID: '1.2.840.113619.1.131'
SOPClassUID: '1.2.840.10008.5.1.4.1.1.128'
SOPInstanceUID: [1x49 char]
StudyDate: '20130514'
SeriesDate: '20130514'
AcquisitionDate: '20130514'
ContentDate: '20130522'
StudyTime: '142911'
SeriesTime: '143208.00'
AcquisitionTime: '143208.00'
ContentTime: '171655'
AccessionNumber: ''
Modality: 'PT'
Manufacturer: 'GE MEDICAL SYSTEMS'
InstitutionName: 'NHS TRUST'
ReferringPhysicianName: [1x1 struct]
StationName: 'dst01'
StudyDescription: ''
SeriesDescription: 'WB_3D_VuePoint'
PhysicianReadingStudy: [1x1 struct]
OperatorName: [1x1 struct]
ManufacturerModelName: 'Discovery STE'
Private_0009_GroupLength: 2714
Private_0009_10xx_Creator: 'GEMS_PETD_01'
Private_0009_11xx_Creator: 'GEMS_GENIE_1'
Private_0009_1002: 'SOLID_TEST'
Private_0009_1005: '20130514143030.00'
Private_0009_1006: 0
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Private_0009_100d: '20130514143208.00'
Private_0009_100e: '20130514143055.00'
Private_0009_1013: [1x59 char]
Private_0009_1014: 'Sternal Notch'
Private_0009_1015: 'SN'
Private_0009_1016: 0
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Private_0009_1036: 'FDG -- fluorodeoxyglucose'
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Private_0009_105e: [1x51 char]
Private_0009_105f: 'SOLID_TEST'
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Private_0009_10b2: 2
Private_0009_10b3: 20
Private_0009_10b4: 70
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Private_0009_10e2: 10
Private_0009_10e4: '3D_AC'
Private_0009_10e5: 0
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Private_0009_10eb: 0
Private_0009_10ec: 0
Private_0009_111e: [1x49 char]
Private_0009_1146: [1x49 char]
PatientGroupLength: 96
PatientName: [1x1 struct]
PatientID: 'SOLID_TEST'
PatientBirthDate: ''
PatientSex: ''
PatientAge: ''
PatientSize: 0
PatientWeight: 0
EthnicGroup: ''
AdditionalPatientHistory: ''
Private_0017_GroupLength: 46
Private_0017_10xx_Creator: 'GEMS_PETD_01'
Private_0017_1004: '20130207140047.00'
AcquisitionGroupLength: 230
SliceThickness: 3.2700
AcquisitionTerminationCondition: 'TIME'
AcquisitionStartCondition: 'MANU'
AcquisitionStartConditionData: 0
AcquisitionTerminationConditionData: 0
SoftwareVersion: '41.04'
ProtocolName: 'WB 3D'
TriggerTime: 0
FrameTime: 0
IntervalsAcquired: 0
IntervalsRejected: 0
ReconstructionDiameter: 700
GantryDetectorTilt: 0
FieldOfViewShape: 'CYLINDRICAL RING'
FieldOfViewDimensions: [2x1 double]
CollimatorType: 'NONE'
ActualFrameDuration: 180000
PatientPosition: 'HFS'
Private_0019_GroupLength: 42
Private_0019_10xx_Creator: 'GEMS_PETD_01'
Private_0019_1004: '20130207140602'
RelationshipGroupLength: 322
StudyInstanceUID: [1x51 char]
SeriesInstanceUID: [1x49 char]
StudyID: '6893'
SeriesNumber: 401
InstanceNumber: 22
ImagePositionPatient: [3x1 double]
ImageOrientationPatient: [6x1 double]
FrameOfReferenceUID: [1x59 char]
PositionReferenceIndicator: 'SN'
SliceLocation: 1.8500
ImagePresentationGroupLength: 218
SamplesPerPixel: 1
PhotometricInterpretation: 'MONOCHROME2'
Rows: 128
Columns: 128
PixelSpacing: [2x1 double]
CorrectedImage: [1x40 char]
BitsAllocated: 16
BitsStored: 16
HighBit: 15
PixelRepresentation: 1
SmallestImagePixelValue: 0
LargestImagePixelValue: 32767
RescaleIntercept: 0
RescaleSlope: 0.3555
LossyImageCompression: '00'
Unknown_0040_0000: 158
AcquisitionContextSequence: [1x1 struct]
NuclearAcquisitionGroupLength: 808
EnergyWindowRangeSequence: [1x1 struct]
RadiopharmaceuticalInformationSequence: [1x1 struct]
NumberOfSlices: 47
TypeOfDetectorMotion: 'NONE'
PatientOrientationCodeSequence: [1x1 struct]
PatientOrientationModifierCodeSequence: [1x1 struct]
PatientGantryRelationshipCodeSequence: [1x1 struct]
SeriesType: 'STATIC\IMAGE'
Units: 'BQML'
CountsSource: 'EMISSION'
RandomsCorrectionMethod: 'SING'
AttenuationCorrectionMethod: 'measured,, 0.096000 cm-1,'
DecayCorrection: 'START'
ReconstructionMethod: '3D IR'
DetectorLinesOfResponseUsed: '0'
ScatterCorrectionMethod: 'Model Based'
AxialMash: [2x1 double]
TransverseMash: 2
CoincidenceWindowWidth: 0
FrameReferenceTime: 0
PrimaryPromptsCountsAccumulated: 0
SecondaryCountsAccumulated: 0
SliceSensitivityFactor: 1
DecayFactor: 1.0095
DoseCalibrationFactor: 1139
ScatterFractionFactor: 0.3174
DeadTimeFactor: 1.1243
ImageIndex: 26
PixelDataGroupLength: 32780
