Dear all,
Currently I am trying to extract the acquisition information needed
for eddy (I am not running topup, as I do not have blib-up-blip-down
b0s) from a GE dicom image. The DTI data was acquired with 6 b0 and
60 DWI.
And I would very much appreciate your thoughts on this to see if
what I am doing is correct.
1. Parameter: FSL (Siemens?) calls this the EPI Factor, while GE
might call it Imaging Frequency?
2. An InPlanePhaseEncodingDirection of 'COL', does this mean
P>>A (posterior to anterior)? The b0 images look like they
were acquired in that way, with frontal lobe distortions towards the
front etc.
3. Also, to acquire the Echo Spacing I simply calculate
1/PixelBandwidth.
Do these statements/questions seem reasonable to you? Please find
the extracted values in bold at the output below from dicominfo
(MATLAB) extracted from the GE dicom.
Best wishes and thank you,
Barbara
dicominfo('/Volumes/NEW_VOLUME/KREILKAMP-NEURO-220/Scans/REF005p/SE6/IM0')
ans =
Filename:
'/Volumes/NEW_VOLUME/KREILKAMP-NEURO-220/Refractory_Scans/REF005p/SE6/IM0'
FileModDate: '20-Jan-2015 09:53:16'
FileSize: 145730
Format: 'DICOM'
FormatVersion: 3
Width: 256
Height: 256
BitDepth: 16
ColorType: 'grayscale'
FileMetaInformationGroupLength: 206
FileMetaInformationVersion: [2x1 uint8]
MediaStorageSOPClassUID:
'1.2.840.10008.5.1.4.1.1.4'
MediaStorageSOPInstanceUID:
'1.2.840.113619.2.353.2807.1585365.14563.1421221817.333'
TransferSyntaxUID: '1.2.840.10008.1.2.1'
ImplementationClassUID: '1.2.840.113619.6.286'
ImplementationVersionName: 'AW4_6_05_003_SLE'
SourceApplicationEntityTitle: 'DVMR-01'
IdentifyingGroupLength: 802
SpecificCharacterSet: 'ISO_IR 100'
ImageType:
'ORIGINAL\PRIMARY\OTHER'
SOPClassUID:
'1.2.840.10008.5.1.4.1.1.4'
SOPInstanceUID:
'1.2.840.113619.2.353.2807.1585365.14563.1421221817.333'
StudyDate: '20150114'
SeriesDate: '20150114'
AcquisitionDate: '20150114'
ContentDate: '20150114'
StudyTime: '104454'
SeriesTime: '111433'
AcquisitionTime: '111433'
ContentTime: '111433'
AccessionNumber: ''
Modality: 'MR'
Manufacturer: 'GE MEDICAL SYSTEMS'
InstitutionName: ''
ReferringPhysicianName: [1x1 struct]
StationName: 'MR01DV01'
StudyDescription: 'MR BRAIN'
SeriesDescription: '2mm DTI 60 dir. PURE'
ManufacturerModelName: 'DISCOVERY MR750'
ReferencedPerformedProcedureStepSequence: [1x1 struct]
ReferencedImageSequence: [1x1 struct]
Private_0009_GroupLength: 150
Private_0009_10xx_Creator: 'GEMS_IDEN_01'
Private_0009_1002: 'MR01'
Private_0009_1004: 'SIGNA'
Private_0009_1027: 1421234073
Private_0009_1030: '10307mrs03'
Private_0009_1031: '9999'
Private_0009_10e3:
'1.2.840.113619.1.353.5.2807.1585365'
Private_0009_10e9: 1421234073
PatientGroupLength: 84
PatientName: [1x1 struct]
PatientID: 'REF005'
PatientBirthDate: '19530904'
PatientSex: 'F'
PatientAge: '061Y'
PatientWeight: 76
AdditionalPatientHistory: ''
AcquisitionGroupLength: 498
ScanningSequence: 'EP\SE'
SequenceVariant: 'NONE'
ScanOptions:
'SAT_GEMS\EPI_GEMS\FILTERED_GEMS\ACC_GEMS\PFF\FS'
MRAcquisitionType: '2D'
AngioFlag: 'N'
SliceThickness: 2
RepetitionTime: 8000
EchoTime: 82.1000
NumberOfAverages: 1
ImagingFrequency: 127.7236
ImagedNucleus: '1H'
EchoNumber: 1
MagneticFieldStrength: 3
SpacingBetweenSlices: 2
EchoTrainLength: 1
PercentSampling: 100
PercentPhaseFieldOfView: 100
PixelBandwidth: 1.9531e+03
DeviceSerialNumber: '00000010307mrs03'
SoftwareVersion: '24\LX\MR Software
release:DV24.0_R01_1344.a'
ProtocolName: ''
HeartRate: 0
CardiacNumberOfImages: 0
TriggerWindow: 0
ReconstructionDiameter: 240
ReceiveCoilName: '32Ch Head'
AcquisitionMatrix: [4x1 uint16]
InPlanePhaseEncodingDirection: 'COL'
FlipAngle: 90
VariableFlipAngleFlag: 'N'
SAR: 0.9978
PatientPosition: 'HFS'
Private_0019_GroupLength: 1166
Private_0019_10xx_Creator: 'GEMS_ACQU_01'
Private_0019_100f: 418.8000
Private_0019_1011: 0
Private_0019_1012: 0
Private_0019_1017: 2
Private_0019_1018: 'S'
Private_0019_1019: 4.4591
Private_0019_101a: 'S'
Private_0019_101b: 134.4590
Private_0019_101e: 240
Private_0019_105a: 536000128
Private_0019_107d: 0
Private_0019_107e: 1
Private_0019_107f: 0
Private_0019_1081: 1
Private_0019_1084: 1.9955
Private_0019_1087: 0
Private_0019_1088: 0
Private_0019_108a: 13
Private_0019_108b: 15
Private_0019_108d: 0
Private_0019_108f: 1
Private_0019_1090: 0
Private_0019_1091: 0
Private_0019_1092: 0
Private_0019_1093: 1.2772e+09
Private_0019_1094: 139
Private_0019_1095: 13
Private_0019_1096: 15
Private_0019_1097: 393760
Private_0019_109b: 1
Private_0019_109c: 'epi2'
Private_0019_109d: '20131029211811'
Private_0019_109e: 'EPI2'
Private_0019_109f: 3
Private_0019_10a0: 0
Private_0019_10a1: 0
Private_0019_10a2: 19456
Private_0019_10a3: 0
Private_0019_10a4: 1
Private_0019_10a7: 1
Private_0019_10a8: 0
Private_0019_10a9: 0
Private_0019_10aa: 0
Private_0019_10ab: 0
Private_0019_10ac: 1
Private_0019_10ad: 0
Private_0019_10ae: 0
Private_0019_10af: 0
Private_0019_10b0: 0
Private_0019_10b1: 0
Private_0019_10b2: 0
Private_0019_10b3: 0
Private_0019_10b4: 0
Private_0019_10b5: 0
Private_0019_10b6: 0
Private_0019_10b7: 0
Private_0019_10b8: 0
Private_0019_10b9: 0
Private_0019_10ba: 0
Private_0019_10bb: 0
Private_0019_10bc: 0
Private_0019_10bd: 0
Private_0019_10be: 0
Private_0019_10c0: 0
Private_0019_10c2: 9990
Private_0019_10c3: 9990
Private_0019_10c4: 9990
Private_0019_10c5: 9990
Private_0019_10c6: 9990
Private_0019_10c7: 9990
Private_0019_10c8: 0
Private_0019_10c9: 0
Private_0019_10ca: 0
Private_0019_10cb: 0
Private_0019_10cc: 0
Private_0019_10cd: 0
Private_0019_10ce: 2
Private_0019_10cf: 0
Private_0019_10d2: 0
Private_0019_10d3: ''
Private_0019_10d5: 3
Private_0019_10d7: 0
Private_0019_10d8: 0
Private_0019_10d9: 0
Private_0019_10df: 6
Private_0019_10e0: 60
Private_0019_10e2: 0
Private_0019_10f2: 0
Private_0019_10f9: 139
RelationshipGroupLength: 362
StudyInstanceUID:
'1.2.840.113619.6.353.158389476855861678793866910246163120775'
SeriesInstanceUID:
'1.2.840.113619.2.353.2807.1585365.17833.1421221747.261'
StudyID: '25361'
SeriesNumber: 7
AcquisitionNumber: 1
InstanceNumber: 1
ImagePositionPatient: [3x1 double]
ImageOrientationPatient: [6x1 double]
FrameOfReferenceUID:
'1.2.840.113619.2.353.2807.1585365.17833.1421221747.251'
Laterality: ''
ImagesInAcquisition: 4356
PositionReferenceIndicator: ''
SliceLocation: 4.4591
StackID: '1'
InStackPositionNumber: 1
Private_0021_GroupLength: 298
Private_0021_10xx_Creator: 'GEMS_RELA_01'
Private_0021_1035: 1
Private_0021_1036: 8
Private_0021_1037: 16
Private_0021_104f: 66
Private_0021_1050: 0
Private_0021_1051: 0
Private_0021_1052: 0
Private_0021_1053: 0
Private_0021_1056: 0
Private_0021_1057: 0
Private_0021_1058: 0
Private_0021_1059: 0
Private_0021_105a: 16
Private_0021_105b: 0
Private_0021_105c: 0
Private_0021_105d: 0
Private_0021_105e: 0
Private_0021_105f: 0
Private_0021_1081: 0
Private_0021_1082: 0
Private_0021_1083: 0
Private_0021_1084: 0
Private_0023_GroupLength: 98
Private_0023_10xx_Creator: 'GEMS_STDY_01'
Private_0023_1070: 0
Private_0023_1074: 0
Private_0023_107d: 0
Private_0023_1080: [1x1 struct]
Private_0025_GroupLength: 998
Private_0025_10xx_Creator: 'GEMS_SERS_01'
Private_0025_1006: 0
Private_0025_1007: 4356
Private_0025_1010: 0
Private_0025_1011: 1
Private_0025_1014: 0
Private_0025_1017: 0
Private_0025_1018: 0
Private_0025_1019: 4356
Private_0025_101a: 'MR01DV01'
Private_0025_101b: [858x1 uint8]
Private_0027_GroupLength: 150
Private_0027_10xx_Creator: 'GEMS_IMAG_01'
Private_0027_1006: 0
Private_0027_1010: 0
Private_0027_1030: ''
Private_0027_1031: 1
Private_0027_1032: 0
Private_0027_1033: 1140850720
Private_0027_1035: 2
Private_0027_1040: 'S'
Private_0027_1041: 4.4591
Private_0027_1060: 128
Private_0027_1061: 128
Private_0027_1062: 1
ImagePresentationGroupLength: 156
SamplesPerPixel: 1
PhotometricInterpretation: 'MONOCHROME2'
Rows: 256
Columns: 256
PixelSpacing: [2x1 double]
BitsAllocated: 16
BitsStored: 16
HighBit: 15
PixelRepresentation: 1
SmallestImagePixelValue: 0
LargestImagePixelValue: 5662
WindowCenter: 2831
WindowWidth: 5662
Private_0029_GroupLength: 102
Private_0029_10xx_Creator: 'GEMS_IMPS_01'
Private_0029_1015: 0
Private_0029_1016: 0
Private_0029_1017: 0
Private_0029_1018: 0
Private_0029_1026: 2
Private_0029_1034: 16384
Private_0029_1035: 0
Unknown_0040_0000: 98
PerformedStationName: 'MR01DV01'
PerformedLocation: 'MR01'
PerformedProcedureStepStartDate: '20150114'
PerformedProcedureStepStartTime: '104423'
PerformedProcedureStepID: '2893.1421232263'
PerformedProcedureStepDescription: 'MR BRAIN'
Private_0043_GroupLength: 9154
Private_0043_10xx_Creator: 'GEMS_PARM_01'
Private_0043_1001: 0
Private_0043_1002: 2
Private_0043_1003: 10
Private_0043_1004: -24
Private_0043_1006: 1
Private_0043_1007: 0
Private_0043_1008: 0
Private_0043_1009: 0
Private_0043_100a: 1
Private_0043_100b: 0
Private_0043_100c: 100
Private_0043_100d: 99.7700
Private_0043_100e: 78.3300
Private_0043_1010: 0
Private_0043_101c: 0
Private_0043_101d: 0
Private_0043_1028: [80x1 uint8]
Private_0043_1029: [2068x1 uint8]
Private_0043_102a: [5648x1 uint8]
Private_0043_102c: 712
Private_0043_102d: 'p+'
Private_0043_102e: ''
Private_0043_102f: 0
Private_0043_1030: 14
Private_0043_1032: 2
Private_0043_1033: 0
Private_0043_1034: 0
Private_0043_1035: 2
Private_0043_1036: 0
Private_0043_1037: 0
Private_0043_1038: [24x1 single]
Private_0043_1039: [4x1 double]
Private_0043_1060: [8x1 double]
Private_0043_1061:
'1.2.840.113619.6.353.158389476855861678793866910246163120775'
Private_0043_1062: '25361'
Private_0043_106f: [4x1 double]
Private_0043_107d: 0
Private_0043_1080:
'A:0\P1:\MRIIWRPnWfRpDO6fWDbSZ5CCue4GysIA\820000000baa310f\P2:0\P3:0\P4:0'
Private_0043_1081: 'C-GE_32Ch Head'
Private_0043_1082:
'SRMode=200\GCoilType=8\gradientAmp=8920\lineFreq=50\RFampType=15\Derat...'
Private_0043_1083: [2x1 double]
Private_0043_1084:
'10000\7\2\1\asset\YES\ASSET'
Private_0043_1088:
'1.2.840.113619.2.353.2807.1585365.17833.1421221747.252'
Private_0043_1089:
'IEC\IEC_FIRST_LEVEL\IEC_FIRST_LEVEL'
Private_0043_108a: 'COL'
Private_0043_1090:
'WHOLE_BODY_6_MIN\LOCAL_PEAK_6_MIN\PARTIAL_BODY_6MIN'
Private_0043_1091: [3x1 double]
Private_0043_1095: 'TG/s1'
Private_0043_1096: 'PRODUCT'
Private_0043_1097: '2\1\1.5 0.2 0.2 2.0
64 0.4 1.05\1.5 0.2 0.2 2.0 64 0.4 1.05\1.5 0.2 0....'
Private_0043_1098:
'1.2.840.113619.2.353.2807.1585365.17833.1421221747.252'
Private_0043_109a: 1
Private_0043_10aa:
'rev=2;a=1;b=10.0;c=0.0;d=1.0;e=0.00;f=12.00\rev=2;g=64.0;h=10.0;i=2.0'
Private_0043_10b3: 0
PixelDataGroupLength: 131084
