[Loris-dev] LORIS Error: The target directory does not contain a single DICOM file.
Morales Pinzon, Alfredo
AMORALESPINZON at bwh.harvard.edu
Mon Dec 2 13:33:17 EST 2019
Hi Cécile,
Apparently the changes we made, fixed StudyInstanceUID and StudyID, worked as we don’t see the error “The target directory does not contain a single DICOM file” anymore. However, now I am getting the following error for all the cases that were fixed:
----------------------------------
Running now the following command: /xxx/bin/mri/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl/> -profile prod -upload_id 20925 /yyy/AAA10001_111222_baseline.tar.gz -verbose Spool message is: The Scan for the uploadID 20925 has already been run with tarchiveID: 20738. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /xxx/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose
----------------------------------
When I run the suggested command line I get the following message:
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$ /xxx/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose
md5sum /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar
PSCID is: AAA10001
CandID id: 111222
visit_label is: baseline
candidate id 111222
PSCID is: AAA10001
CandID id: 111222
visit_label is: baseline
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Number of MINC files that will be considered for inserting into the database: 0
No data could be converted into valid MINC files. Localizers will not be considered!
----------------------------------
I tested the conversion of one the DICOM folder to minc and then executed mincinfo but I didn’t get any errors.
Do you know why this might be happening?
Is there an issue with the files created by LORIS in the first attempt I tried to upload these images (see uploadId 20925)?
Let me know if you need more information from my side to help overcome this issue.
Best regards,
Alfredo.
On Nov 25, 2019, at 10:25 AM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:
Hi Cécile,
Thank you for your prompt response. We will make the changes, try again, and report back to this thread.
Best regards,
Alfredo.
On Nov 25, 2019, at 10:06 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
External Email - Use Caution
Hi Alfredo,
Indeed, the StudyInstanceUID needs to have a value for the insertion pipeline to work so that could explain the no DICOM found error.
FYI - StudyInstanceUID also needs to be unique for each uploaded study otherwise insertion in the tarchive tables would fail with the error: "the study has already been uploaded"
Hope this helps,
Cécile
On Mon, Nov 25, 2019 at 10:02 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,
I am batch uploading images to imaging visits using the script batch_uploads_imageuploader but for some images I get the following error:
The target directory does not contain a single DICOM file.
I had seen this error previously due to missing dicom fields like StudyID (0020,0010) and ImagePositionPatient (0020,0032). However, after checking these particular dicom fields and setting StudyID it to '0' I am still getting the same error. What other dicom fields should I check?
Is there a log where I can exactly find the error? Does the "StudyInstanceUID" need to have a value?
I'm pasting the dcmdump of a dicom at the end of this email in case this might help figuring out what is the issue.
I am using LORIS v at 20.1.1.<mailto:v at 20.1.1.>
Thank you in advance for your help.
Best regards,
Alfredo.
--------------------------------------------------------------------------------------
# Dicom-File-Format
# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 230 # 4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion
(0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianImplicit # 18, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0] # 28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_360] # 16, 1 ImplementationVersionName
(0002,0016) AE [GDCM/ITK 3.17.0] # 16, 1 SourceApplicationEntityTitle
# Dicom-Data-Set
# Used TransferSyntax: Little Endian Implicit
(0008,0008) CS [DERIVED\SECONDARY] # 18, 2 ImageType
(0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID
(0008,0018) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 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 (no value available) # 0, 0 StudyTime
(0008,0031) TM [085517] # 6, 1 SeriesTime
(0008,0032) TM [085517] # 6, 1 AcquisitionTime
(0008,0060) CS [MR] # 2, 1 Modality
(0008,0070) LO [AAABBBCCC] # 6, 1 Manufacturer
(0008,0104) LO [Anonymized] # 10, 1 CodeMeaning
(0008,103e) LO [t1c] # 4, 1 SeriesDescription
(0008,1090) LO [nifti2dicom] # 12, 1 ManufacturerModelName
(0010,0010) PN [10041] # 6, 1 PatientName
(0010,0020) LO [10041] # 6, 1 PatientID
(0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID
(0010,0030) DA [19650101] # 8, 1 PatientBirthDate
(0010,0040) CS [Anonymized] # 10, 1 PatientSex
(0010,1010) AS [Anonymized] # 10, 1 PatientAge
(0010,1030) DS (no value available) # 0, 0 PatientWeight
(0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence
(0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence
(0010,21f0) LO [Anonymized] # 10, 1 PatientReligiousPreference
(0012,0050) LO [baseline] # 8, 1 ClinicalTrialTimePointID
(0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved
(0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod
(0018,0050) DS [3] # 2, 1 SliceThickness
(0018,0088) DS [3] # 2, 1 SpacingBetweenSlices
(0020,000d) UI (no value available) # 0, 0 StudyInstanceUID
(0020,000e) UI [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] # 64, 1 SeriesInstanceUID
(0020,0010) SH [0] # 2, 1 StudyID
(0020,0011) IS [901] # 4, 1 SeriesNumber
(0020,0012) IS [1] # 2, 1 AcquisitionNumber
(0020,0013) IS [1] # 2, 1 InstanceNumber
(0020,0020) CS [L\R] # 4, 2 PatientOrientation
(0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] # 50, 3 ImagePositionPatient
(0020,0037) DS [1\0\0\0\1\0] # 12, 6 ImageOrientationPatient
(0020,0052) UI [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] # 64, 1 FrameOfReferenceUID
(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 [1\1] # 4, 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
(0032,1033) LO [Anonymized] # 10, 1 RequestingService
(0040,0280) ST [Anonymized] # 10, 1 CommentsOnThePerformedProcedureStep
(0400,0563) LO [Anonymized] # 10, 1 ModifyingSystem
(0400,0564) LO [Anonymized] # 10, 1 SourceOfPreviousValues
(0400,0565) CS [Anonymized] # 10, 1 ReasonForTheAttributeModification
(1110,21b0) ?? 0a\00 # 2, 1 Unknown Tag & Data
(7fe0,0010) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 131072, 1 PixelData
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