[MINC-users] dicom3_to_minc failing on some Siemens data sets...
Jon Harlap
jharlap at bic.mni.mcgill.ca
Tue May 29 07:45:36 EDT 2007
Hi Michel,
This is because DICOMperl (the library upon which dicom3_to_minc is
based) does not support DICOM sequences with undefined length. I'd
suggest that you either:
a) use dcm2mnc (included with MINC) to convert your data instead of
dicom3_to_minc.
b) or try to use dcmtk (dcmconv or dcmodify) to fix the sequence's
length info to be defined.
Cheers,
J
Audette, Michel wrote:
> Hi everyone,
>
> I have stumbled on some Siemens data sets on which dicom3_to_minc seems to fail...
>
> I am seeing ERROR: Code SQ, length (some number that does not make sense)
> Wrong number of bits allocated per image()
>
> Using DicomDumper, I have reproduced the header below. DicomWorks is able to visualize the data.
>
> Can anyone suggest a means of debugging this and/or a simple workaround? Thanks for your help.
>
> Cheers,
>
> Michel
>
> P.S.: DicomDumper cut-and-paste:
>
> (0002,0000) [Group Length] --> VR: UL, VL: 4
> Value: 204
> (0002,0001) [File Meta Information Version] --> VR: OB, VL: 2
> Value: [string of bytes]
> (0002,0002) [Media Storage SOP Class UID] --> VR: UI, VL: 26
> Value: 1.2.840.10008.5.1.4.1.1.2
> (0002,0003) [Media Storage SOP Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0002,0010) [Transfer Syntax UID] --> VR: UI, VL: 20
> Value: 1.2.840.10008.1.2.1
> (0002,0012) [Implementation Class UID] --> VR: UI, VL: 20
> Value: 1.2.276.0.19.1996.1
> (0002,0013) [Implementation Version Name] --> VR: SH, VL: 14
> Value: VTServer 4.32
> (0002,0016) [Source Application Entity Title] --> VR: AE, VL: 16
> Value: AN_CT38357
> (0008,0000) [Group Length] --> VR: UL, VL: 4
> Value: 754
> (0008,0005) [Specific Character Set] --> VR: CS, VL: 10
> Value: ISO_IR 100
> (0008,0008) [Image Type] --> VR: CS, VL: 34
> Value: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
> (0008,0016) [SOP Class UID] --> VR: UI, VL: 26
> Value: 1.2.840.10008.5.1.4.1.1.2
> (0008,0018) [SOP Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0008,0020) [Study Date] --> VR: DA, VL: 8
> Value: 20070404
> (0008,0021) [Series Date] --> VR: DA, VL: 8
> Value: 20070404
> (0008,0022) [Acquisition Date] --> VR: DA, VL: 8
> Value: 20070404
> (0008,0023) [Content Date] --> VR: DA, VL: 8
> Value: 20070404
> (0008,0030) [Study Time] --> VR: TM, VL: 14
> Value: 161137.390000
> (0008,0031) [Series Time] --> VR: TM, VL: 6
> Value: 161252
> (0008,0032) [Acquisition Time] --> VR: TM, VL: 14
> Value: 161301.963478
> (0008,0033) [Content Time] --> VR: TM, VL: 14
> Value: 161301.963478
> (0008,0050) [Accession Number] --> VR: SH, VL: 0
> Value:
> (0008,0060) [Modality] --> VR: CS, VL: 2
> Value: CT
> (0008,0070) [Manufacturer] --> VR: LO, VL: 8
> Value: SIEMENS
> (0008,0080) [Institution Name] --> VR: LO, VL: 30
> Value: Rad.Nuk.med.Gemeischaftspraxis
> (0008,0081) [Institution Address] --> VR: ST, VL: 50
> Value: Johannisplatz
> Leipzig/2f0cd3/
> Leipzig
> Deutschland
> (0008,0090) [Referring Physician's Name] --> VR: PN, VL: 0
> Value:
> (0008,1010) [Station Name] --> VR: SH, VL: 8
> Value: CT38357
> (0008,1030) [Study Description] --> VR: LO, VL: 20
> Value: Schädel^09_Brainlab
> (0008,103E) [Series Description] --> VR: LO, VL: 14
> Value: axial 2.0 H40s
> (0008,1090) [Manufacturer's Model Name] --> VR: LO, VL: 8
> Value: Balance
> (0008,1140) [Referenced Image Sequence] --> VR: SQ, VL: 4294967295
> Value: [sequence of elements]
> * Item 1
> (0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 26
> Value: 1.2.840.10008.5.1.4.1.1.2
> (0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217900015152526
> (0008,2112) [Source Image Sequence] --> VR: SQ, VL: 4294967295
> Value: [sequence of elements]
> * Item 1
> (0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 20
> Value: 1.3.12.2.1107.5.9.1
> (0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217905113681033
> (0009,0000) [Group Length] --> VR: UL, VL: 4
> Value: 28
> (0009,0010) [Unknown Name] --> VR: LO, VL: 20
> Value: SIEMENS CT VA1 DUMMY
> (0010,0000) [Group Length] --> VR: UL, VL: 4
> Value: 94
> (0010,0010) [Patient's Name] --> VR: PN, VL: 18
> Value: Köhler^Wolfgang^^^
> (0010,0020) [Patient Id] --> VR: LO, VL: 6
> Value: 69128
> (0010,0030) [Patient's Birth Date] --> VR: DA, VL: 8
> Value: 19350307
> (0010,0040) [Patient's Sex] --> VR: CS, VL: 2
> Value: M
> (0010,1010) [Patient's Age] --> VR: AS, VL: 4
> Value: 072Y
> (0010,1020) [Patient's Size] --> VR: DS, VL: 0
> Value:
> (0010,1030) [Patient's Weight] --> VR: DS, VL: 0
> Value:
> (0018,0000) [Group Length] --> VR: UL, VL: 4
> Value: 262
> (0018,0015) [Body Part Examined] --> VR: CS, VL: 4
> Value: HEAD
> (0018,0050) [Slice Thickness] --> VR: DS, VL: 2
> Value: 2
> (0018,0060) [KVP] --> VR: DS, VL: 4
> Value: 130
> (0018,1020) [Software Version(s)] --> VR: LO, VL: 6
> Value: VA47C
> (0018,1030) [Protocol Name] --> VR: LO, VL: 12
> Value: 09_Brainlab
> (0018,1100) [Reconstruction Diameter] --> VR: DS, VL: 4
> Value: 282
> (0018,1110) [Distance Source to Detector] --> VR: DS, VL: 4
> Value: 940
> (0018,1111) [Distance Source to Patient] --> VR: DS, VL: 4
> Value: 535
> (0018,1120) [Gantry/Detector Tilt] --> VR: DS, VL: 2
> Value: 0
> (0018,1130) [Table Height] --> VR: DS, VL: 4
> Value: 160
> (0018,1140) [Rotation Direction] --> VR: CS, VL: 2
> Value: CW
> (0018,1150) [Exposure Time] --> VR: IS, VL: 4
> Value: 1000
> (0018,1151) [X-ray Tube Current] --> VR: IS, VL: 2
> Value: 90
> (0018,1152) [Exposure] --> VR: IS, VL: 2
> Value: 90
> (0018,1160) [Filter Type] --> VR: SH, VL: 2
> Value: 1
> (0018,1170) [Generator Power] --> VR: IS, VL: 2
> Value: 11
> (0018,1190) [Focal Spot(s)] --> VR: DS, VL: 4
> Value: 0.95
> (0018,1200) [Date of Last Calibration] --> VR: DA, VL: 8
> Value: 20070404
> (0018,1201) [Time of Last Calibration] --> VR: TM, VL: 14
> Value: 060159.000000
> (0018,1210) [Convolution Kernel] --> VR: SH, VL: 4
> Value: H40s
> (0018,5100) [Patient Position] --> VR: CS, VL: 4
> Value: HFS
> (0019,0000) [Group Length] --> VR: UL, VL: 4
> Value: 38
> (0019,0010) [Unknown Name] --> VR: LO, VL: 20
> Value: SIEMENS CT VA0 COAD
> (0019,10B0) [Unknown Name] --> VR: DS, VL: 2
> Value: 2
> (0020,0000) [Group Length] --> VR: UL, VL: 4
> Value: 284
> (0020,000D) [Study Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217453428112303
> (0020,000E) [Series Instance UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217907287251360
> (0020,0010) [Study Id] --> VR: SH, VL: 2
> Value: 2
> (0020,0011) [Series Number] --> VR: IS, VL: 2
> Value: 2
> (0020,0012) [Acquisition Number] --> VR: IS, VL: 2
> Value: 2
> (0020,0013) [Instance Number] --> VR: IS, VL: 2
> Value: 1
> (0020,0032) [Image Position (Patient)] --> VR: DS, VL: 26
> Value: -140.72461\-317.72461\-160
> (0020,0037) [Image Orientation (Patient)] --> VR: DS, VL: 12
> Value: 1\0\0\0\1\0
> (0020,0052) [Frame of Reference UID] --> VR: UI, VL: 46
> Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217896016622697
> (0020,1040) [Position Reference Indicator] --> VR: LO, VL: 0
> Value:
> (0020,1041) [Slice Location] --> VR: DS, VL: 4
> Value: -160
> (0020,4000) [Image Comments] --> VR: LT, VL: 0
> Value:
> (0021,0000) [Group Length] --> VR: UL, VL: 4
> Value: 34
> (0021,0010) [Unknown Name] --> VR: LO, VL: 12
> Value: SIEMENS MED
> (0021,1011) [Unknown Name] --> VR: DS, VL: 6
> Value: 0\-17
> (0028,0000) [Group Length] --> VR: UL, VL: 4
> Value: 198
> (0028,0002) [Samples per Pixel] --> VR: US, VL: 2
> Value: 1
> (0028,0004) [Photometric Interpretation] --> VR: CS, VL: 12
> Value: MONOCHROME2
> (0028,0010) [Rows] --> VR: US, VL: 2
> Value: 512
> (0028,0011) [Columns] --> VR: US, VL: 2
> Value: 512
> (0028,0030) [Pixel Spacing] --> VR: DS, VL: 22
> Value: 0.55078125\0.55078125
> (0028,0100) [Bits Allocated] --> VR: US, VL: 2
> Value: 16
> (0028,0101) [Bits Stored] --> VR: US, VL: 2
> Value: 12
> (0028,0102) [High Bit] --> VR: US, VL: 2
> Value: 11
> (0028,0103) [Pixel Representation] --> VR: US, VL: 2
> Value: 0
> (0028,1050) [Window Center] --> VR: DS, VL: 6
> Value: 40\700
> (0028,1051) [Window Width] --> VR: DS, VL: 8
> Value: 200\3200
> (0028,1052) [Rescale Intercept] --> VR: DS, VL: 6
> Value: -1024
> (0028,1053) [Rescale Slope] --> VR: DS, VL: 2
> Value: 1
> (0028,1055) [Window Center & Width Explanation] --> VR: LO, VL: 16
> Value: WINDOW1\WINDOW2
> (0029,0000) [Group Length] --> VR: UL, VL: 4
> Value: 560
> (0029,0010) [Unknown Name] --> VR: LO, VL: 18
> Value: SIEMENS CSA HEADER
> (0029,0011) [Unknown Name] --> VR: LO, VL: 22
> Value: SIEMENS MEDCOM HEADER
> (0029,1008) [Unknown Name] --> VR: CS, VL: 6
> Value: SOM 5
> (0029,1009) [Unknown Name] --> VR: LO, VL: 12
> Value: VA10A 971201
> (0029,1010) [Unknown Name] --> VR: OB, VL: 418
> Value: [string of bytes]
> (0029,1131) [Unknown Name] --> VR: LO, VL: 12
> Value: 4.0.92170301
> (0029,1134) [Unknown Name] --> VR: CS, VL: 12
> Value: DB TO DICOM
> (0032,0000) [Group Length] --> VR: UL, VL: 4
> Value: 28
> (0032,1060) [Requested Procedure Description] --> VR: LO, VL: 20
> Value: Schädel 09_Brainlab
> (0055,0000) [Group Length] --> VR: UL, VL: 4
> Value: 8542
> (0055,0010) [Unknown Name] --> VR: LO, VL: 18
> Value: VEPRO VIF 3.0 DATA
> (0055,1020) [Unknown Name] --> VR: OB, VL: 2048
> Value: [string of bytes]
> (0055,1030) [Unknown Name] --> VR: OB, VL: 6412
> Value: [string of bytes]
> (0055,1065) [Unknown Name] --> VR: OB, VL: 20
> Value: [string of bytes]
> (0059,0000) [Group Length] --> VR: UL, VL: 4
> Value: 274
> (0059,0010) [Unknown Name] --> VR: LO, VL: 24
> Value: VEPRO DICOM TRANSFER 1.0
> (0059,1010) [Unknown Name] --> VR: SQ, VL: 4294967295
> Value: [sequence of elements]
> * Item 1
> (0059,0010) [Unknown Name] --> VR: LO, VL: 28
> Value: VEPRO DICOM RECEIVE DATA 1.0
> (0059,1040) [Unknown Name] --> VR: DA, VL: 8
> Value: 20070404
> (0059,1041) [Unknown Name] --> VR: TM, VL: 6
> Value: 160913
> (0059,1042) [Unknown Name] --> VR: ST, VL: 10
> Value: SIEMENS_CT
> (0059,1043) [Unknown Name] --> VR: ST, VL: 8
> Value: VCONTROL
> (0059,1050) [Unknown Name] --> VR: ST, VL: 8
> Value: vepro102
> (0059,1051) [Unknown Name] --> VR: ST, VL: 16
> Value: VTSERVER
> (0059,1060) [Unknown Name] --> VR: ST, VL: 12
> Value: 10.10.29.53
> (0059,1061) [Unknown Name] --> VR: ST, VL: 10
> Value: AN_CT38357
> (0059,1070) [Unknown Name] --> VR: UI, VL: 20
> Value: 1.2.840.10008.1.2.1
> (7FE0,0000) [Group Length] --> VR: UL, VL: 4
> Value: 524300
> (7FE0,0010) [Pixel Data] --> VR: OW, VL: 524288
> Value: [string of words]
>
>
> Michel Audette, Ph.D.
> Innovation Center Computer Assisted Surgery (ICCAS)
> Philipp-Rosenthal-Strasse 55
> Leipzig, Germany
> Phone: ++49 (0) 341 / 97 - 1 20 13
> Fax: ++49 (0) 341 / 97 - 1 20 09
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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