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Hi Nicolas,
<div class=""><br class="">
</div>
<div class="">Thank you for your answer and suggestion. We will try the conversion and report the results.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Nov 26, 2019, at 7:14 AM, Nicolas Brossard <<a href="mailto:nicolasbrossard.mni@gmail.com" class="">nicolasbrossard.mni@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p>
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</div>
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">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:</div>
<div class=""><br class="">
</div>
<div class=""><font face="monospace" class="">dcmdjpeg <my_file> <my_file></font></div>
<div class=""><font face="monospace" class=""><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class="">Dcm2mnc on the new converted file will most likely succeed then.</font></div>
<div class=""><font face="arial, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class="">If you have a lot of DICOM files located in a given directory, you can convert them all with one command:</font></div>
<div class=""><font face="arial, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="monospace" class="">find <my_dicom_dir> -type f | xargs -i dcmdjpeg {} {}</font></div>
<div class=""><font face="monospace" class=""><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class="">Let me know how it goes!</font></div>
<div class=""><font face="arial, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class=""><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class="">Cheers,</font></div>
<div class=""><font face="arial, sans-serif" class="">Nicolas</font></div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Nov 25, 2019 at 12:47 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;" class="">Dear LorisDev team,
<div class=""><br class="">
</div>
<div class="">I am having the following error when converting dcm2mnc: </div>
<div class=""><br class="">
</div>
<div class="">----------------------------------------------------------------------------</div>
<div class="">
<div class="">$ dcm2mnc -verbose 094901-00003-Dicom-pdw/ .</div>
<div class=""><br class="">
</div>
<div class="">Expanding directory '094901-00003-Dicom-pdw/'</div>
<div class="">Checking file types...</div>
<div class="">File 094901-00003-Dicom-pdw/0000100012.dcm appears to be DICOM (CD/Export).</div>
<div class="">UNKNOWN DICOM TRANSFER SYNTAX: 1.2.840.10008.1.2.4.57</div>
</div>
<div class="">----------------------------------------------------------------------------</div>
<div class=""><br class="">
</div>
<div class="">Do you know why this might be happening? You may find the dcmdump of one dicom file at the end of this email.</div>
<div class=""><br class="">
</div>
<div class="">Thank you in advance.</div>
<div class=""><br class="">
</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
</div>
<div class="">----------------------------------------------------------------------------</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""># Dicom-File-Format</div>
<div class=""><br class="">
</div>
<div class=""># Dicom-Meta-Information-Header</div>
<div class=""># Used TransferSyntax: Little Endian Explicit</div>
<div class="">(0002,0000) UL 202 # 4, 1 FileMetaInformationGroupLength</div>
<div class="">(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion</div>
<div class="">(0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID</div>
<div class="">(0002,0003) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 MediaStorageSOPInstanceUID</div>
<div class=""><font color="#ff0000" class="">(0002,0010) UI =JPEGLossless:Non-hierarchical:Process14 # 22, 1 TransferSyntaxUID</font></div>
<div class="">(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.1] # 28, 1 ImplementationClassUID</div>
<div class="">(0002,0013) SH [OFFIS_DCMTK_361] # 16, 1 ImplementationVersionName</div>
<div class=""><br class="">
</div>
<div class=""># Dicom-Data-Set</div>
<div class=""># Used TransferSyntax: JPEG Lossless, Non-hierarchical, Process 14</div>
<div class="">(0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet</div>
<div class="">(0008,0008) CS [ORIGINAL\PRIMARY\OTHER] # 22, 3 ImageType</div>
<div class="">(0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID</div>
<div class="">(0008,0018) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 SOPInstanceUID</div>
<div class="">(0008,0020) DA [20000101] # 8, 1 StudyDate</div>
<div class="">(0008,0021) DA [20000101] # 8, 1 SeriesDate</div>
<div class="">(0008,0022) DA [20000101] # 8, 1 AcquisitionDate</div>
<div class="">(0008,0030) TM [094647] # 6, 1 StudyTime</div>
<div class="">(0008,0031) TM [094901] # 6, 1 SeriesTime</div>
<div class="">(0008,0032) TM [094901] # 6, 1 AcquisitionTime</div>
<div class="">(0008,0033) TM [094901] # 6, 1 ContentTime</div>
<div class="">(0008,0060) CS [MR] # 2, 1 Modality</div>
<div class="">(0008,0070) LO [AAABBBCCC] # 18, 1 Manufacturer</div>
<div class="">(0008,0082) SQ (Sequence with explicit length #=0) # 0, 1 InstitutionCodeSequence</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0008,0104) LO [Anonymized] # 10, 1 CodeMeaning</div>
<div class="">(0008,1032) SQ (Sequence with explicit length #=0) # 0, 1 ProcedureCodeSequence</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0008,103e) LO [pdw] # 4, 1 SeriesDescription</div>
<div class="">(0008,1090) LO [Signa HDxt] # 10, 1 ManufacturerModelName</div>
<div class="">(0008,1110) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedStudySequence</div>
<div class=""> (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item</div>
<div class=""> (0008,1150) UI =RETIRED_DetachedStudyManagementSOPClass # 24, 1 ReferencedSOPClassUID</div>
<div class=""> (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.341] # 56, 1 ReferencedSOPInstanceUID</div>
<div class=""> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0008,1111) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedPerformedProcedureStepSequence</div>
<div class=""> (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item</div>
<div class=""> (0008,1150) UI =ModalityPerformedProcedureStepSOPClass # 24, 1 ReferencedSOPClassUID</div>
<div class=""> (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.340] # 56, 1 ReferencedSOPInstanceUID</div>
<div class=""> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0008,1140) SQ (Sequence with explicit length #=3) # 318, 1 ReferencedImageSequence</div>
<div class=""> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item</div>
<div class=""> (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID</div>
<div class=""> (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.285] # 56, 1 ReferencedSOPInstanceUID</div>
<div class=""> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem</div>
<div class=""> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item</div>
<div class=""> (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID</div>
<div class=""> (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.286] # 56, 1 ReferencedSOPInstanceUID</div>
<div class=""> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem</div>
<div class=""> (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item</div>
<div class=""> (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID</div>
<div class=""> (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.287] # 56, 1 ReferencedSOPInstanceUID</div>
<div class=""> (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0010,0010) PN [AAABBBCCC] # 24, 1 PatientName</div>
<div class="">(0010,0020) LO [11111] # 6, 1 PatientID</div>
<div class="">(0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID</div>
<div class="">(0010,0030) DA [19000101] # 8, 1 PatientBirthDate</div>
<div class="">(0010,0040) CS [Anonymized] # 10, 1 PatientSex</div>
<div class="">(0010,1010) AS [Anonymized] # 10, 1 PatientAge</div>
<div class="">(0010,1030) DS [10] # 2, 1 PatientWeight</div>
<div class="">(0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence</div>
<div class="">(0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence</div>
<div class="">(0012,0050) LO [AAABBBCCC] # 8, 1 ClinicalTrialTimePointID</div>
<div class="">(0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved</div>
<div class="">(0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod</div>
<div class="">(0018,0020) CS [SE] # 2, 1 ScanningSequence</div>
<div class="">(0018,0021) CS [SK] # 2, 1 SequenceVariant</div>
<div class="">(0018,0022) CS [FAST_GEMS\EDR_GEMS\TRF_GEMS] # 28, 3 ScanOptions</div>
<div class="">(0018,0023) CS [2D] # 2, 1 MRAcquisitionType</div>
<div class="">(0018,0025) CS [N] # 2, 1 AngioFlag</div>
<div class="">(0018,0050) DS [3] # 2, 1 SliceThickness</div>
<div class="">(0018,0080) DS [2900] # 4, 1 RepetitionTime</div>
<div class="">(0018,0081) DS [9.424] # 6, 1 EchoTime</div>
<div class="">(0018,0082) DS [0] # 2, 1 InversionTime</div>
<div class="">(0018,0083) DS [1] # 2, 1 NumberOfAverages</div>
<div class="">(0018,0084) DS [127.723758] # 10, 1 ImagingFrequency</div>
<div class="">(0018,0085) SH [1H] # 2, 1 ImagedNucleus</div>
<div class="">(0018,0086) IS [1] # 2, 1 EchoNumbers</div>
<div class="">(0018,0087) DS [3] # 2, 1 MagneticFieldStrength</div>
<div class="">(0018,0088) DS [3] # 2, 1 SpacingBetweenSlices</div>
<div class="">(0018,0091) IS [3] # 2, 1 EchoTrainLength</div>
<div class="">(0018,0093) DS [100] # 4, 1 PercentSampling</div>
<div class="">(0018,0094) DS [100] # 4, 1 PercentPhaseFieldOfView</div>
<div class="">(0018,0095) DS [177.578] # 8, 1 PixelBandwidth</div>
<div class="">(0018,1000) LO [056MRE3TH2565370] # 16, 1 DeviceSerialNumber</div>
<div class="">(0018,1020) LO [15\LX\MR Software release:15.0_M4_0910.a] # 40, 3 SoftwareVersions</div>
<div class="">(0018,1088) IS [0] # 2, 1 HeartRate</div>
<div class="">(0018,1090) IS [0] # 2, 1 CardiacNumberOfImages</div>
<div class="">(0018,1094) IS [0] # 2, 1 TriggerWindow</div>
<div class="">(0018,1100) DS [250] # 4, 1 ReconstructionDiameter</div>
<div class="">(0018,1250) SH [AAABBBBRAIN] # 8, 1 ReceiveCoilName</div>
<div class="">(0018,1310) US 0\256\256\0 # 8, 4 AcquisitionMatrix</div>
<div class="">(0018,1312) CS [ROW] # 4, 1 InPlanePhaseEncodingDirection</div>
<div class="">(0018,1314) DS [90] # 2, 1 FlipAngle</div>
<div class="">(0018,1315) CS [N] # 2, 1 VariableFlipAngleFlag</div>
<div class="">(0018,1316) DS [1.3561] # 6, 1 SAR</div>
<div class="">(0018,5100) CS [HFS] # 4, 1 PatientPosition</div>
<div class="">(0020,000d) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.344] # 56, 1 StudyInstanceUID</div>
<div class="">(0020,000e) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.349] # 56, 1 SeriesInstanceUID</div>
<div class="">(0020,0010) SH [35313] # 6, 1 StudyID</div>
<div class="">(0020,0011) IS [3] # 2, 1 SeriesNumber</div>
<div class="">(0020,0012) IS [1] # 2, 1 AcquisitionNumber</div>
<div class="">(0020,0013) IS [1] # 2, 1 InstanceNumber</div>
<div class="">(0020,0032) DS [-130.858\-141.195\94.3036] # 26, 3 ImagePositionPatient</div>
<div class="">(0020,0037) DS [0.999785\-0.0207525\0\0.0207528\0.999767\0.00598169] # 52, 6 ImageOrientationPatient</div>
<div class="">(0020,0052) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.343] # 56, 1 FrameOfReferenceUID</div>
<div class="">(0020,0060) CS (no value available) # 0, 0 Laterality</div>
<div class="">(0020,1002) IS [55] # 2, 1 ImagesInAcquisition</div>
<div class="">(0020,1040) LO (no value available) # 0, 0 PositionReferenceIndicator</div>
<div class="">(0020,1041) DS [95.04837036] # 12, 1 SliceLocation</div>
<div class="">(0020,9056) SH [1] # 2, 1 StackID</div>
<div class="">(0020,9057) UL 1 # 4, 1 InStackPositionNumber</div>
<div class="">(0028,0002) US 1 # 2, 1 SamplesPerPixel</div>
<div class="">(0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation</div>
<div class="">(0028,0010) US 256 # 2, 1 Rows</div>
<div class="">(0028,0011) US 256 # 2, 1 Columns</div>
<div class="">(0028,0030) DS [0.9766\0.9766] # 14, 2 PixelSpacing</div>
<div class="">(0028,0100) US 16 # 2, 1 BitsAllocated</div>
<div class="">(0028,0101) US 16 # 2, 1 BitsStored</div>
<div class="">(0028,0102) US 15 # 2, 1 HighBit</div>
<div class="">(0028,0103) US 1 # 2, 1 PixelRepresentation</div>
<div class="">(0028,0106) SS 0 # 2, 1 SmallestImagePixelValue</div>
<div class="">(0028,0107) SS 133 # 2, 1 LargestImagePixelValue</div>
<div class="">(0028,1050) DS [66] # 2, 1 WindowCenter</div>
<div class="">(0028,1051) DS [133] # 4, 1 WindowWidth</div>
<div class="">(0032,1033) LO [Anonymized] # 10, 1 RequestingService</div>
<div class="">(0040,0253) SH [MR1354787338] # 12, 1 PerformedProcedureStepID</div>
<div class="">(0040,0260) SQ (Sequence with explicit length #=0) # 0, 1 PerformedProtocolCodeSequence</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem</div>
<div class="">(0040,0280) ST [Anonymized] # 10, 1 CommentsOnThePerformedProcedureStep</div>
<div class="">(1110,21b0) UN 0a\00 # 2, 1 Unknown Tag & Data</div>
<div class="">(7fe0,0010) OB (PixelSequence #=2) # u/l, 1 PixelData</div>
<div class=""> (fffe,e000) pi 00\00\00\00 # 4, 1 Item</div>
<div class=""> (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</div>
<div class="">(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem</div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="webkit-block-placeholder">
</div>
<p class="">The information in this e-mail is intended only for the person to whom it is<br class="">
addressed. If you believe this e-mail was sent to you in error and the e-mail<br class="">
contains patient information, please contact the Partners Compliance HelpLine at<br class="">
<a href="http://www.partners.org/complianceline" target="_blank" class="">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br class="">
but does not contain patient information, please contact the sender and properly<br class="">
dispose of the e-mail.</p>
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