[Gate-users] Hdr/Img file and HU value
刘斌信件
golder_time at 163.com
Sun Aug 25 12:19:26 CEST 2013
Hi everyone,
I use ImageJ to convert sequences of CT images to hdr/img format file. Some vital information of header file and image file are different between my converted hdr/img files and examples in web. The difference concentrate in “ Dimensions, PixelDimensions, Orientation ” in header file and lower limit of HU value in image file. I think the HU value is wrong in the converted imgae files
Any one give me guideline how to set parameter of ImageJ to convert CT file ? I hope that the derived hdr/img file will suit for simulating in GATE.
The following are outputs of header file and raw data of my converted hdr/img file and the example included files respectively .
Converted hdr/img information :
Filename: 'IMJysrCT2.5.hdr'
FileModDate: '23-八月-2013 15:28:43'
HdrFileSize: 348
ImgFileSize: 36175872
Format: 'Analyze'
FormatVersion: '7.5'
Width: 512
Height: 512
BitDepth: 16
ColorType: 'grayscale'
ByteOrder: 'ieee-be'
HdrDataType: ''
DatabaseName: ''
Extents: 16384
SessionError: 0
Regular: 1
Dimensions: [512 512 69 1 1]
VoxelUnits: 'mm'
CalibrationUnits: ''
ImgDataType: 'DT_SIGNED_SHORT'
PixelDimensions: [1.0742 1.0742 2.5000]
VoxelOffset: 0
CalibrationMax: 81
CalibrationMin: -20
Compressed: 0
Verified: 0
GlobalMax: 65535
GlobalMin: 0
Descriptor: ''
AuxFile: ''
Orientation: 'Transverse unflipped'
Originator: ''
Generated: ''
Scannumber: ''
PatientID: ''
ExposureDate: ''
ExposureTime: ''
Views: 0
VolumesAdded: 0
StartField: 0
FieldSkip: 0
OMax: 0
OMin: 0
SMax: 0
SMin: 0
Dimensions: [512 512 69 1 1], PixelDimensions: [1.0742 1.0742 2.5000], Orientation: 'Transverse unflipped'
Part of CT value in image file
-1018 -1023 -1023 -1022 -1020 -1020 -1019 -1021 -1014 -1018 -1021 -1024 -1019 -1019 -3024 -3024 -3024 -3024 -3024
-1021 -1018 -1021 -1024 -1020 -1021 -1017 -1021 -1016 -1016 -1016 -1023 -1024 -1024 -3024 -3024 -3024 -3024 -3024
-1021 -1020 -1022 -1019 -1021 -1022 -1022 -1019 -1017 -1016 -1020 -1020 -1023 -3024 -3024 -3024 -3024 -3024 -3024
-1018 -1022 -1024 -1020 -1019 -1019 -1022 -1021 -1020 -1020 -1018 -1020 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1021 -1024 -1021 -1021 -1021 -1022 -1018 -1021 -1019 -1023 -1022 -1020 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1020 -1022 -1021 -1022 -1019 -1020 -1018 -1020 -1022 -1021 -1020 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1022 -1017 -1020 -1019 -1019 -1019 -1020 -1018 -1024 -1021 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1019 -1022 -1020 -1017 -1017 -1019 -1023 -1022 -1019 -1021 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1021 -1018 -1017 -1020 -1018 -1020 -1018 -1024 -1022 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1023 -1018 -1018 -1019 -1019 -1019 -1023 -1021 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1019 -1018 -1023 -1020 -1021 -1018 -1020 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024
-1019 -1018 -1020 -1024 -1020 -1021 -1016 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -3024 -302
I think the HU value (HU=-3024 ) is wrong , because the minimum HU value of air is between -1000 and -1050 .
The web example information:
Filename: 'patient1-2mm.hdr'
FileModDate: '12- November-2009 16:34:44'
HdrFileSize: 348
ImgFileSize: 3524472
Format: 'Analyze'
FormatVersion: '7.5'
Width: 126
Height: 126
BitDepth: 16
ColorType: 'grayscale'
ByteOrder: 'ieee-le'
HdrDataType: 'SHORT N'
DatabaseName: ''
Extents: 16384
SessionError: 0
Regular: 1
Dimensions: [126 126 111 1 1 1 1]
VoxelUnits: ''
CalibrationUnits: ''
ImgDataType: 'DT_SIGNED_SHORT'
PixelDimensions: [2 2 2 1 1 1 1]
VoxelOffset: 0
CalibrationMax: 0
CalibrationMin: 0
Compressed: 0
Verified: 0
GlobalMax: 0
GlobalMin: 0
Descriptor: ''
AuxFile: ''
Orientation: 'Coronal unflipped'
Originator: ''
Generated: ''
Scannumber: ''
PatientID: ''
ExposureDate: ''
ExposureTime: ''
Views: 0
VolumesAdded: 0
StartField: 0
FieldSkip: 0
OMax: 0
OMin: 0
SMax: 0
SMin: 0
Dimensions: [126 126 111 1 1 1 1],PixelDimensions: [2 2 2 1 1 1 1], Orientation: 'Coronal unflipped'.
I don't understand why the dimension value is seven , what the " [ 1 1 1 1]" is mean , how to set the orientation to 'Coronal unflipped'.
Part of CT value in image file
-1001 -1001 -1001 -1001 -1000 -1000 -1000 -1000 -1000 -1000 -1000 -1000
-1001 -1001 -1001 -1001 -1001 -1001 -1000 -1000 -1000 -1000 -1000 -1000
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1000 -1000 -1001 -1000 -1000
-1001 -1001 -1001 -1001 -1001 -1001 -1000 -1001 -1001 -1001 -1001 -1000
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1000 -1000
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1000 -1001
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1000 -1001
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1000 -1001
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001
-1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001 -1001
I am very grateful to your help .
Sincerely yours,
Bin
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