Error Loading MRI Files

Support
, , , ,
1

Operating system: Windows 10
Slicer version: 4.8/4.9
Expected behavior: Be able to 3d model mri scan
Actual behavior: Cant see the scans at all when loading

So I have tried using my own mri scans and a friend’s mri scans from 2 different imaging centers and the same error occurs. I am unable to load the series to make it a full image and then make into a 3d model as well. Other viewers work but I cant 3d render with those. What should I do? It says there is no pixel attributions every time i try to examine.

2

image
image2048×1092 166 KB

How do I over come these errors?

3

image
image2048×1092 213 KB

And when I try loading, this pops up.

4

Does it load correctly if you select a single series (e.g., SeriesNumber 3, 4, 5, 6, 7, or 8 only) and click Load?

If you select a single series and click Metadata button, can you see a slider in the window that pops up? if yes, what is the range of the slider? (1 / …? displayed on the right side of the slider)
Could you click on Copy metadata button and past the result here? Make sure to remove all patient identifiable information - name, birth date, patient ID, etc.

5

image
image2048×1092 450 KB

this is if i load 1 series. The pictures are blurry and when i scroll through it looks like rains is falling while only displaying a single picture.

6

[0008,0000] GenericGroupLength 1406 UL 4
[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType [5] DERIVED, PRIMARY, M, DIS2D, JP2K LOSSY 6:1 CS 38
[0008,0012] InstanceCreationDate 20170804 DA 8
[0008,0013] InstanceCreationTime 153202.562 TM 10
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,0018] SOPInstanceUID 1.2.840.113837.225093149.20170804154425.3 UI 42
[0008,0020] StudyDate 20170804 DA 8
[0008,0021] SeriesDate 20170804 DA 8
[0008,0022] AcquisitionDate 20170804 DA 8
[0008,0023] ContentDate 20170804 DA 8
[0008,0030] StudyTime 152601.562 TM 10
[0008,0031] SeriesTime 153202.531 TM 10
[0008,0032] AcquisitionTime 152813.5875 TM 12
[0008,0033] ContentTime 153202.562 TM 10
[0008,0050] AccessionNumber 03303523 SH 8
[0008,0060] Modality MR CS 2
[0008,0070] Manufacturer LO 0
[0008,0080] InstitutionName LO 12
[0008,0081] InstitutionAddress 52
[0008,0090] ReferringPhysicianName PN 18
[0008,1010] StationName MRC31439 SH 8
[0008,1030] StudyDescription MR SHOULDER WO DYE RIGHT LO 24
[0008,1032] ProcedureCodeSequence SQ 84
[fffe,e000] Item na 68
[0008,0100] CodeValue 73221 SH R SH 10
[0008,0102] CodingSchemeDesignator 73221 SH R SH 10
[0008,0104] CodeMeaning MR SHOULDER WO DYE RIGHT LO 24
[0008,103e] SeriesDescription pd_blade_FS_AX _320 LO 20
[0008,1040] InstitutionalDepartmentName Clinic LO 6
[0008,1048] PhysiciansOfRecord PN 18
[0008,1050] PerformingPhysicianName PN 0
[0008,1070] OperatorsName RP PN 2
[0008,1090] ManufacturerModelName Espree LO 6
[0008,1110] ReferencedStudySequence SQ 94
[fffe,e000] Item na 78
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.3.1.2.3.1 UI 24
[0008,1155] ReferencedSOPInstanceUID 1.2.840.113837.1592560075.1501881959.3 UI 38
[0008,1120] ReferencedPatientSequence SQ 32
[fffe,e000] Item na 16
[0008,1150] ReferencedSOPClassUID UI 0
[0008,1155] ReferencedSOPInstanceUID UI 0
[0008,1140] ReferencedImageSequence SQ 330
[fffe,e000] Item na 94
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,1155] ReferencedSOPInstanceUID 1.3.12.2.1107.5.2.31.31439.2017080415271043912449763 UI 52
[fffe,e000] Item na 94
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,1155] ReferencedSOPInstanceUID 1.3.12.2.1107.5.2.31.31439.2017080415265594998349731 UI 52
[fffe,e000] Item na 94
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,1155] ReferencedSOPInstanceUID 1.3.12.2.1107.5.2.31.31439.2017080415263090299549720 UI 52
[0008,2111] DerivationDescription LOSSY JPEG 2000 COMPRESSION 6:1 (AMICAS) ST 40
[0008,2112] SourceImageSequence SQ 110
[fffe,e000] Item na 94
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,0018] SOPInstanceUID 1.3.12.2.1107.5.2.31.31439.2017080415320196130550085 UI 52
[0010,0000] GenericGroupLength 210 UL 4
[0010,0010] PatientName PN 14
[0010,0020] PatientID LO 6
[0010,0021] IssuerOfPatientID LO 4
[0010,0030] PatientBirthDate DA 8
[0010,0040] PatientSex F CS 2
[0010,1000] RETIRED_OtherPatientIDs LO 12
[0010,1010] PatientAge AS 4
[0010,1030] PatientWeight DS 14
[0010,1040] PatientAddress 36
[0010,2154] PatientTelephoneNumbers SH 14
[0010,21b0] AdditionalPatientHistory LT 0
[0010,4000] PatientComments LT 0
[0018,0000] GenericGroupLength 426 UL 4
[0018,0015] BodyPartExamined SHOULDER CS 8
[0018,0020] ScanningSequence SE CS 2
[0018,0021] SequenceVariant [3] SK, SP, OSP CS 10
[0018,0022] ScanOptions FS CS 2
[0018,0023] MRAcquisitionType 2D CS 2
[0018,0024] SequenceName tseB2d1_11 SH 12
[0018,0025] AngioFlag N CS 2
[0018,0050] SliceThickness 3 DS 2
[0018,0080] RepetitionTime 3000 DS 4
[0018,0081] EchoTime 48 DS 2
[0018,0083] NumberOfAverages 1 DS 2
[0018,0084] ImagingFrequency 63.653639 DS 10
[0018,0085] ImagedNucleus 1H SH 2
[0018,0086] EchoNumbers 1 IS 2
[0018,0087] MagneticFieldStrength 1.5 DS 4
[0018,0088] SpacingBetweenSlices 3.75 DS 4
[0018,0089] NumberOfPhaseEncodingSteps 320 IS 4
[0018,0091] EchoTrainLength 11 IS 2
[0018,0093] PercentSampling 100 DS 4
[0018,0094] PercentPhaseFieldOfView 100 DS 4
[0018,0095] PixelBandwidth 260 DS 4
[0018,1000] DeviceSerialNumber 31439 LO 6
[0018,1020] SoftwareVersions syngo MR B19 LO 12
[0018,1030] ProtocolName pd_blade_FS_AX _320 LO 20
[0018,1251] TransmitCoilName Body SH 4
[0018,1310] AcquisitionMatrix [4] 320, 0, 0, 320 US 8
[0018,1312] InPlanePhaseEncodingDirection COL CS 4
[0018,1314] FlipAngle 150 DS 4
[0018,1315] VariableFlipAngleFlag N CS 2
[0018,1316] SAR 1.1928163770324 DS 16
[0018,1318] dBdt 0 DS 2
[0018,5100] PatientPosition HFS CS 4
[0019,0000] PrivateGroupLength 216 UL 4
[0019,0010] PrivateCreator SIEMENS MR HEADER LO 18
[0019,1008] Unknown Tag & Data IMAGE NUM 4 CS 12
[0019,1009] Unknown Tag & Data 1.0 LO 4
[0019,100b] Unknown Tag & Data 225985 DS 6
[0019,100f] Unknown Tag & Data Fast SH 4
[0019,1011] Unknown Tag & Data No SH 2
[0019,1012] Unknown Tag & Data [3] 0, 0, -1231 SL 12
[0019,1013] Unknown Tag & Data [3] 0, 0, -1221 SL 12
[0019,1014] Unknown Tag & Data [3] 0, 0, 10 IS 6
[0019,1015] Unknown Tag & Data [3] -217.26391602000001, -64.745762830000004, -35.913135529999998 FD 24
[0019,1016] Unknown Tag & Data 1.505 DS 6
[0019,1017] Unknown Tag & Data 1 DS 2
[0019,1018] Unknown Tag & Data 6000 IS 4
[0020,0000] GenericGroupLength 330 UL 4
[0020,000d] StudyInstanceUID 1.2.840.113837.3779700918.1501881959.2 UI 38
[0020,000e] SeriesInstanceUID 1.3.12.2.1107.5.2.31.31439.2017080415320180937050053.0.0.0 UI 58
[0020,0010] StudyID yw0w6kooz SH 10
[0020,0011] SeriesNumber 3 IS 2
[0020,0012] AcquisitionNumber 1 IS 2
[0020,0013] InstanceNumber 20 IS 2
[0020,0032] ImagePositionPatient [3] -217.26391601563, -64.745762825012, -25.913135528564 DS 50
[0020,0037] ImageOrientationPatient [6] 1, 0, 0, 0, 1, 0 DS 12
[0020,0052] FrameOfReferenceUID 1.3.12.2.1107.5.2.31.31439.2.20170804152601718.0.0.0 UI 52
[0020,1040] PositionReferenceIndicator LO 0
[0020,1041] SliceLocation -25.913135528564 DS 16
[0023,0000] PrivateGroupLength 198 UL 4
[0023,0010] PrivateCreator AMICAS0 LO 8
[0023,1001] Unknown Tag & Data 1.3.12.2.1107.5.2.31.31439.2017080415320196130550085 UI 52
[0023,1008] Unknown Tag & Data 0 US 2
[0023,1010] Unknown Tag & Data 1967 US 2
[0023,1016] Unknown Tag & Data 0 SL 4
[0023,1021] Unknown Tag & Data 1 US 2
[0023,1022] Unknown Tag & Data 2902 UL 4
[0023,1045] Unknown Tag & Data 3 US 2
[0023,1054] Unknown Tag & Data MRC31439\MGPACS2 ST 16
[0023,1055] Unknown Tag & Data RP LO 2
[0023,1065] Unknown Tag & Data MergeHealthCare LO 16
[0028,0000] GenericGroupLength 184 UL 4
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0010] Rows 320 US 2
[0028,0011] Columns 320 US 2
[0028,0030] PixelSpacing [2] 0.5, 0.5 DS 8
[0028,0100] BitsAllocated 16 US 2
[0028,0101] BitsStored 12 US 2
[0028,0102] HighBit 11 US 2
[0028,0103] PixelRepresentation 0 US 2
[0028,1050] WindowCenter 442 DS 4
[0028,1051] WindowWidth 1087 DS 4
[0028,1055] WindowCenterWidthExplanation Algo1 LO 6
[0028,2110] LossyImageCompression 01 CS 2
[0028,2112] LossyImageCompressionRatio 6 DS 2
[0028,2114] LossyImageCompressionMethod ISO_15444_1 CS 12
[0029,0000] PrivateGroupLength 69898 UL 4
[0029,0010] PrivateCreator SIEMENS CSA HEADER LO 18
[0029,0011] PrivateCreator SIEMENS MEDCOM HEADER2 LO 22
[0029,1008] CSAImageHeaderType IMAGE NUM 4 CS 12
[0029,1009] CSAImageHeaderVersion 20170804 LO 8
[0029,1010] CSAImageHeaderInfo 53 OB 9468
[0029,1018] CSASeriesHeaderType MR CS 2
[0029,1019] CSASeriesHeaderVersion 20170804 LO 8
[0029,1020] CSASeriesHeaderInfo 53 OB 60276
[0029,1160] SeriesWorkflowStatus com LO 4
[0032,0000] GenericGroupLength 162 UL 4
[0032,1032] RequestingPhysician PN 18
[0032,1060] RequestedProcedureDescription MR SHOULDER WO DYE RIGHT LO 24
[0032,1064] RequestedProcedureCodeSequence SQ 84
[fffe,e000] Item na 68
[0008,0100] CodeValue 73221 SH R SH 10
[0008,0102] CodingSchemeDesignator 73221 SH R SH 10
[0008,0104] CodeMeaning MR SHOULDER WO DYE RIGHT LO 24
[0040,0000] GenericGroupLength 292 UL 4
[0040,0244] PerformedProcedureStepStartDate 20170804 DA 8
[0040,0245] PerformedProcedureStepStartTime 152601.656 TM 10
[0040,0253] PerformedProcedureStepID yw0w6kop0 SH 10
[0040,0254] PerformedProcedureStepDescription MR SHOULDER WO DYE RIGHT LO 24
[0040,0275] RequestAttributesSequence SQ 184
[fffe,e000] Item na 168
[0040,0007] ScheduledProcedureStepDescription MR SHOULDER WO DYE RIGHT LO 24
[0040,0008] ScheduledProtocolCodeSequence SQ 84
[fffe,e000] Item na 68
[0008,0100] CodeValue 73221 SH R SH 10
[0008,0102] CodingSchemeDesignator 73221 SH R SH 10
[0008,0104] CodeMeaning MR SHOULDER WO DYE RIGHT LO 24
[0040,0009] ScheduledProcedureStepID yw0w6kop0 SH 10
[0040,1001] RequestedProcedureID yw0w6kooz SH 10
[0051,0000] PrivateGroupLength 220 UL 4
[0051,0010] PrivateCreator SIEMENS MR HEADER LO 18
[0051,1008] Unknown Tag & Data IMAGE NUM 4 CS 12
[0051,1009] Unknown Tag & Data 1.0 LO 4
[0051,100a] Unknown Tag & Data TA 03:45 LO 8
[0051,100b] Unknown Tag & Data 320320 LO 8
[0051,100c] Unknown Tag & Data FoV 160*160 LO 12
[0051,100d] Unknown Tag & Data SP F25.9 SH 8
[0051,100e] Unknown Tag & Data Tra LO 4
[0051,100f] Unknown Tag & Data C:SH LO 4
[0051,1012] Unknown Tag & Data TP H10 SH 6
[0051,1013] Unknown Tag & Data +LPH SH 4
[0051,1016] Unknown Tag & Data M/DIS2D LO 8
[0051,1017] Unknown Tag & Data SL 3.0 SH 6
[0051,1019] Unknown Tag & Data A1/FS LO 6
[7fe0,0000] GenericGroupLength 34126 UL 4
[7fe0,0010] PixelData OB 0

7

1/20 sliders is the range of the sliders for a single series metadata

8

Probably the issue is that the image is compressed.

Potential solutions:

  1. Set DICOM reader to GDCM and try to load again (menu: Edit/Application settings/DICOM/DICOM reader approach)

  2. Download DCMTK toolkit and use dcmdjpeg utility to decompress each file