[Loris-dev] Error dcm2mnc: UNKNOWN DICOM TRANSFER SYNTAX
Nicolas Brossard
nicolasbrossard.mni at gmail.com
Tue Nov 26 07:14:06 EST 2019
Hi Alfredo,
As you can see from the dcmdump output you provided, your file's
TransferSyntaxUID is JPEGLossless and it looks like dcm2mnc does not like
that. You can try converting your DICOM file so that it has a
TransferSyntaxUID set to LittleEndianExplicit, like this:
dcmdjpeg <my_file> <my_file>
Dcm2mnc on the new converted file will most likely succeed then.
If you have a lot of DICOM files located in a given directory, you can
convert them all with one command:
find <my_dicom_dir> -type f | xargs -i dcmdjpeg {} {}
Let me know how it goes!
Cheers,
Nicolas
On Mon, Nov 25, 2019 at 12:47 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:
> Dear LorisDev team,
>
> I am having the following error when converting dcm2mnc:
>
>
> ----------------------------------------------------------------------------
> $ dcm2mnc -verbose 094901-00003-Dicom-pdw/ .
>
> Expanding directory '094901-00003-Dicom-pdw/'
> Checking file types...
> File 094901-00003-Dicom-pdw/0000100012.dcm appears to be DICOM (CD/Export).
> UNKNOWN DICOM TRANSFER SYNTAX: 1.2.840.10008.1.2.4.57
>
> ----------------------------------------------------------------------------
>
> Do you know why this might be happening? You may find the dcmdump of one
> dicom file at the end of this email.
>
> Thank you in advance.
>
> Alfredo.
>
>
> ----------------------------------------------------------------------------
>
> # Dicom-File-Format
>
> # Dicom-Meta-Information-Header
> # Used TransferSyntax: Little Endian Explicit
> (0002,0000) UL 202 # 4, 1
> FileMetaInformationGroupLength
> (0002,0001) OB 00\01 # 2, 1
> FileMetaInformationVersion
> (0002,0002) UI =MRImageStorage # 26, 1
> MediaStorageSOPClassUID
> (0002,0003) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] #
> 56, 1 MediaStorageSOPInstanceUID
> (0002,0010) UI =JPEGLossless:Non-hierarchical:Process14 # 22, 1
> TransferSyntaxUID
> (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.1] # 28, 1
> ImplementationClassUID
> (0002,0013) SH [OFFIS_DCMTK_361] # 16, 1
> ImplementationVersionName
>
> # Dicom-Data-Set
> # Used TransferSyntax: JPEG Lossless, Non-hierarchical, Process 14
> (0008,0005) CS [ISO_IR 100] # 10, 1
> SpecificCharacterSet
> (0008,0008) CS [ORIGINAL\PRIMARY\OTHER] # 22, 3 ImageType
> (0008,0016) UI =MRImageStorage # 26, 1
> SOPClassUID
> (0008,0018) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] #
> 56, 1 SOPInstanceUID
> (0008,0020) DA [20000101] # 8, 1 StudyDate
> (0008,0021) DA [20000101] # 8, 1 SeriesDate
> (0008,0022) DA [20000101] # 8, 1
> AcquisitionDate
> (0008,0030) TM [094647] # 6, 1 StudyTime
> (0008,0031) TM [094901] # 6, 1 SeriesTime
> (0008,0032) TM [094901] # 6, 1
> AcquisitionTime
> (0008,0033) TM [094901] # 6, 1
> ContentTime
> (0008,0060) CS [MR] # 2, 1 Modality
> (0008,0070) LO [AAABBBCCC] # 18, 1 Manufacturer
> (0008,0082) SQ (Sequence with explicit length #=0) # 0, 1
> InstitutionCodeSequence
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0008,0104) LO [Anonymized] # 10, 1
> CodeMeaning
> (0008,1032) SQ (Sequence with explicit length #=0) # 0, 1
> ProcedureCodeSequence
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0008,103e) LO [pdw] # 4, 1
> SeriesDescription
> (0008,1090) LO [Signa HDxt] # 10, 1
> ManufacturerModelName
> (0008,1110) SQ (Sequence with explicit length #=1) # 104, 1
> ReferencedStudySequence
> (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item
> (0008,1150) UI =RETIRED_DetachedStudyManagementSOPClass # 24, 1
> ReferencedSOPClassUID
> (0008,1155) UI
> [1.2.840.113619.2.244.3596.11861676.21950.1354710592.341] # 56, 1
> ReferencedSOPInstanceUID
> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0
> ItemDelimitationItem
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0008,1111) SQ (Sequence with explicit length #=1) # 104, 1
> ReferencedPerformedProcedureStepSequence
> (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item
> (0008,1150) UI =ModalityPerformedProcedureStepSOPClass # 24, 1
> ReferencedSOPClassUID
> (0008,1155) UI
> [1.2.840.113619.2.244.3596.11861676.21950.1354710592.340] # 56, 1
> ReferencedSOPInstanceUID
> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0
> ItemDelimitationItem
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0008,1140) SQ (Sequence with explicit length #=3) # 318, 1
> ReferencedImageSequence
> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item
> (0008,1150) UI =MRImageStorage # 26, 1
> ReferencedSOPClassUID
> (0008,1155) UI
> [1.2.840.113619.2.244.3596.11861676.21355.1354711179.285] # 56, 1
> ReferencedSOPInstanceUID
> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0
> ItemDelimitationItem
> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item
> (0008,1150) UI =MRImageStorage # 26, 1
> ReferencedSOPClassUID
> (0008,1155) UI
> [1.2.840.113619.2.244.3596.11861676.21355.1354711179.286] # 56, 1
> ReferencedSOPInstanceUID
> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0
> ItemDelimitationItem
> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item
> (0008,1150) UI =MRImageStorage # 26, 1
> ReferencedSOPClassUID
> (0008,1155) UI
> [1.2.840.113619.2.244.3596.11861676.21355.1354711179.287] # 56, 1
> ReferencedSOPInstanceUID
> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0
> ItemDelimitationItem
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0010,0010) PN [AAABBBCCC] # 24, 1 PatientName
> (0010,0020) LO [11111] # 6, 1 PatientID
> (0010,0021) LO [Anonymized] # 10, 1
> IssuerOfPatientID
> (0010,0030) DA [19000101] # 8, 1
> PatientBirthDate
> (0010,0040) CS [Anonymized] # 10, 1 PatientSex
> (0010,1010) AS [Anonymized] # 10, 1 PatientAge
> (0010,1030) DS [10] # 2, 1
> PatientWeight
> (0010,2150) LO [Anonymized] # 10, 1
> CountryOfResidence
> (0010,2152) LO [Anonymized] # 10, 1
> RegionOfResidence
> (0012,0050) LO [AAABBBCCC] # 8, 1
> ClinicalTrialTimePointID
> (0012,0062) CS [Yes] # 4, 1
> PatientIdentityRemoved
> (0012,0063) LO [Genentech] # 10, 1
> DeidentificationMethod
> (0018,0020) CS [SE] # 2, 1
> ScanningSequence
> (0018,0021) CS [SK] # 2, 1
> SequenceVariant
> (0018,0022) CS [FAST_GEMS\EDR_GEMS\TRF_GEMS] # 28, 3
> ScanOptions
> (0018,0023) CS [2D] # 2, 1
> MRAcquisitionType
> (0018,0025) CS [N] # 2, 1 AngioFlag
> (0018,0050) DS [3] # 2, 1
> SliceThickness
> (0018,0080) DS [2900] # 4, 1
> RepetitionTime
> (0018,0081) DS [9.424] # 6, 1 EchoTime
> (0018,0082) DS [0] # 2, 1
> InversionTime
> (0018,0083) DS [1] # 2, 1
> NumberOfAverages
> (0018,0084) DS [127.723758] # 10, 1
> ImagingFrequency
> (0018,0085) SH [1H] # 2, 1
> ImagedNucleus
> (0018,0086) IS [1] # 2, 1
> EchoNumbers
> (0018,0087) DS [3] # 2, 1
> MagneticFieldStrength
> (0018,0088) DS [3] # 2, 1
> SpacingBetweenSlices
> (0018,0091) IS [3] # 2, 1
> EchoTrainLength
> (0018,0093) DS [100] # 4, 1
> PercentSampling
> (0018,0094) DS [100] # 4, 1
> PercentPhaseFieldOfView
> (0018,0095) DS [177.578] # 8, 1
> PixelBandwidth
> (0018,1000) LO [056MRE3TH2565370] # 16, 1
> DeviceSerialNumber
> (0018,1020) LO [15\LX\MR Software release:15.0_M4_0910.a] # 40, 3
> SoftwareVersions
> (0018,1088) IS [0] # 2, 1 HeartRate
> (0018,1090) IS [0] # 2, 1
> CardiacNumberOfImages
> (0018,1094) IS [0] # 2, 1
> TriggerWindow
> (0018,1100) DS [250] # 4, 1
> ReconstructionDiameter
> (0018,1250) SH [AAABBBBRAIN] # 8, 1
> ReceiveCoilName
> (0018,1310) US 0\256\256\0 # 8, 4
> AcquisitionMatrix
> (0018,1312) CS [ROW] # 4, 1
> InPlanePhaseEncodingDirection
> (0018,1314) DS [90] # 2, 1 FlipAngle
> (0018,1315) CS [N] # 2, 1
> VariableFlipAngleFlag
> (0018,1316) DS [1.3561] # 6, 1 SAR
> (0018,5100) CS [HFS] # 4, 1
> PatientPosition
> (0020,000d) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.344] #
> 56, 1 StudyInstanceUID
> (0020,000e) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.349] #
> 56, 1 SeriesInstanceUID
> (0020,0010) SH [35313] # 6, 1 StudyID
> (0020,0011) IS [3] # 2, 1
> SeriesNumber
> (0020,0012) IS [1] # 2, 1
> AcquisitionNumber
> (0020,0013) IS [1] # 2, 1
> InstanceNumber
> (0020,0032) DS [-130.858\-141.195\94.3036] # 26, 3
> ImagePositionPatient
> (0020,0037) DS [0.999785\-0.0207525\0\0.0207528\0.999767\0.00598169] #
> 52, 6 ImageOrientationPatient
> (0020,0052) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.343] #
> 56, 1 FrameOfReferenceUID
> (0020,0060) CS (no value available) # 0, 0 Laterality
> (0020,1002) IS [55] # 2, 1
> ImagesInAcquisition
> (0020,1040) LO (no value available) # 0, 0
> PositionReferenceIndicator
> (0020,1041) DS [95.04837036] # 12, 1
> SliceLocation
> (0020,9056) SH [1] # 2, 1 StackID
> (0020,9057) UL 1 # 4, 1
> InStackPositionNumber
> (0028,0002) US 1 # 2, 1
> SamplesPerPixel
> (0028,0004) CS [MONOCHROME2] # 12, 1
> PhotometricInterpretation
> (0028,0010) US 256 # 2, 1 Rows
> (0028,0011) US 256 # 2, 1 Columns
> (0028,0030) DS [0.9766\0.9766] # 14, 2
> PixelSpacing
> (0028,0100) US 16 # 2, 1
> BitsAllocated
> (0028,0101) US 16 # 2, 1 BitsStored
> (0028,0102) US 15 # 2, 1 HighBit
> (0028,0103) US 1 # 2, 1
> PixelRepresentation
> (0028,0106) SS 0 # 2, 1
> SmallestImagePixelValue
> (0028,0107) SS 133 # 2, 1
> LargestImagePixelValue
> (0028,1050) DS [66] # 2, 1
> WindowCenter
> (0028,1051) DS [133] # 4, 1
> WindowWidth
> (0032,1033) LO [Anonymized] # 10, 1
> RequestingService
> (0040,0253) SH [MR1354787338] # 12, 1
> PerformedProcedureStepID
> (0040,0260) SQ (Sequence with explicit length #=0) # 0, 1
> PerformedProtocolCodeSequence
> (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0
> SequenceDelimitationItem
> (0040,0280) ST [Anonymized] # 10, 1
> CommentsOnThePerformedProcedureStep
> (1110,21b0) UN 0a\00 # 2, 1 Unknown
> Tag & Data
> (7fe0,0010) OB (PixelSequence #=2) # u/l, 1 PixelData
> (fffe,e000) pi 00\00\00\00 # 4, 1 Item
> (fffe,e000) pi
> ff\d8\ff\fe\00\26\43\6f\6d\70\72\65\73\73\65\64\20\62\79\20\44\69... #
> 50160, 1 Item
> (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0
> SequenceDelimitationItem
>
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