Hi?
I’ve loaded DICOM images acquired from CCTA.
As you can see below images, sagittal and coronal views look like compressed (not real thickness) when using 3D slicing. But those views are normal when using InVesalius.
Please let me know how to solve this problem.
Thanks.
Thanks for reporting this.
Could you please try if the image is loaded correctly in the latest nightly version of Slicer?
If it does not work, could you give additional information:
- How did you load the image: by importing it into the DICOM database and load it from the DICOM browser / using the Data dialog?
- What scanner acquired the image?
Also refer to the techniques listed here:
Thanks for replying.
I’ve tried this with the latest nightly version of 3D Slicer. But it showed same phenomena.
I’ve loaded DICOM images using the Botton shaped [DCM] (Raise the DICOM module…) and then import button. I tried this by ‘copy’ and by ‘add link’.
I don’t understand your last question ‘What scanner…’. Do you mean product name of CT scanner?
I wish you can solve this problem.
Thanks.
Thank you. I’ll check this.
Yes, what brand and model? Some scanner models known to have DICOM conformance problems and older other scanners often used varying slice spacing.
Do you get any warning about potential geometry issues when you load the image?
If you click on the Advanced option in the DICOM browser and click Examine, what is in the DICOM data column in the first line (that has a checked checkbox)?
Thank you, Mr. Andras Lasso.
I don’t know the exact brand and model. But probably from GE.
During loading, I did not receive any warning sign.
On the advanced option, the first column shows like this
DICOM data: [v] 80656: AXI 75% 62-56-62
Reader: Scalar Volume
Warnings: none
Also you can use the “Metadata” button to look at the dicom headers. There you can see the manufacturer and other useful information.
To make it easier to share the metadata with us for analysis, I’ve added the option to copy the metadata to clipboard. Could you please download the latest nightly version of Slicer now (if you downloaded Slicer yesterday or before then it is too old, it does not contain this feature yet), and then:
- Open DICOM browser
- Select the image that you want to load
- Check Advanced checkbox
- Click Examine button
- Click Metadata button
- Click Copy Metadata button
- Paste the copied text to any text editor
- Remove patient name, birthdate, ID, and all other patient identifiable information
- Copy-paste the metadata here so that we can have a look
Thnaks, Mr. Iassoan.
I paste the metadata.
[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType [3] DERIVED, SECONDARY, AQNETSC CS 26
[0008,0012] InstanceCreationDate 20170717 DA 8
[0008,0013] InstanceCreationTime 143957 TM 6
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.7 UI 26
[0008,0018] SOPInstanceUID 2.16.840.1.113669.632.21.4079790272.20170717.364973997.0.97414.1 UI 64
[0008,0020] StudyDate 20170717 DA 8
[0008,0021] SeriesDate 20170717 DA 8
[0008,0022] AcquisitionDate 20170717 DA 8
[0008,0030] StudyTime 141020 TM 6
[0008,0031] SeriesTime 143957 TM 6
[0008,0032] AcquisitionTime 141827 TM 6
[0008,0050] AccessionNumber E20170086239 SH 12
[0008,0060] Modality CT CS 2
[0008,0064] ConversionType WSD CS 4
[0008,0070] Manufacturer Philips LO 8
[0008,0080] InstitutionName ***************************** LO 20
[0008,0090] ReferringPhysicianName ***************************** PN 12
[0008,1010] StationName CT-95305 SH 8
[0008,1030] StudyDescription CT Cardiac Angiography[3D] LO 26
[0008,1032] ProcedureCodeSequence SQ 82
[fffe,e000] Item na 66
[0008,0100] CodeValue 2CGC05CAD SH 10
[0008,0102] CodingSchemeDesignator BROKER SH 6
[0008,0104] CodeMeaning CT Cardiac Angiography[3D] LO 26
[0008,103e] SeriesDescription HEART 75% LO 10
[0008,1110] ReferencedStudySequence SQ 0
[0009,0000] PrivateGroupLength 14 UL 4
[0009,0010] PrivateCreator GEIIS LO 6
[0010,0010] PatientName ***************************** PN 12
[0010,0020] PatientID ***************************** LO 8
[0010,0021] IssuerOfPatientID ***************************** LO 24
[0010,0030] PatientBirthDate ***************************** DA 8
[0010,0040] PatientSex ***************************** CS 2
[0010,1040] PatientAddress ì ìë¡14 2 LO 14
[0018,1012] DateOfSecondaryCapture 20170717 DA 8
[0018,1014] TimeOfSecondaryCapture 143957 TM 6
[0018,1016] SecondaryCaptureDeviceManufacturer TERARECON LO 10
[0018,1018] SecondaryCaptureDeviceManufacturerModelName AQNET LO 6
[0018,1019] SecondaryCaptureDeviceSoftwareVersions V4.4.7.851 LO 10
[0018,1030] ProtocolName CARDIAC ANGIO/Cardiac LO 22
[0018,5100] PatientPosition FFS CS 4
[0020,000d] StudyInstanceUID 1.2.840.113704.1.111.5572.1500268220.1 UI 38
[0020,000e] SeriesInstanceUID 2.16.840.1.113669.2.1.1.47404864.54.20170717.636359002560781250 UI 64
[0020,0010] StudyID 132221 SH 6
[0020,0011] SeriesNumber 1031 IS 4
[0020,0013] InstanceNumber 1 IS 2
[0020,0020] PatientOrientation CS 0
[0020,0060] Laterality CS 0
[0028,0002] SamplesPerPixel 3 US 2
[0028,0004] PhotometricInterpretation RGB CS 4
[0028,0006] PlanarConfiguration 0 US 2
[0028,0008] NumberOfFrames 1 IS 2
[0028,0010] Rows 1024 US 2
[0028,0011] Columns 1024 US 2
[0028,0030] PixelSpacing [2] 0.2588700056076, 0.2588700056076 DS 32
[0028,0100] BitsAllocated 8 US 2
[0028,0101] BitsStored 8 US 2
[0028,0102] HighBit 7 US 2
[0028,0103] PixelRepresentation 0 US 2
[0032,1033] RequestingService CAR LO 4
[0040,0275] RequestAttributesSequence SQ 36
[fffe,e000] Item na 20
[0040,1001] RequestedProcedureID E20170086239 SH 12
[0040,2017] FillerOrderNumberImagingServiceRequest RAD23 LO 6
This image seems to be just a screenshot. Do you have multiple series in the series list (the list that has “SeriesNumber” as the first column)? Can you send the content (copied as text) for the other series as well? (don’t forget to remove patient information)
Sorry for late response.
I attach metadata of another patient underwent CCTA.
I’ve checked this data set is consisted of multiple series.
Thank your help.
[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType [3] DERIVED, SECONDARY, MIP CS 22
[0008,0012] InstanceCreationDate 20161212 DA 8
[0008,0013] InstanceCreationTime 152552 TM 6
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.7 UI 26
[0008,0018] SOPInstanceUID 1.2.840.113704.7.1.1.8088.1481523952.312 UI 40
[0008,0020] StudyDate 20161212 DA 8
[0008,0022] AcquisitionDate 20161212 DA 8
[0008,0023] ContentDate 20161212 DA 8
[0008,0030] StudyTime 141200 TM 6
[0008,0032] AcquisitionTime 141628 TM 6
[0008,0033] ContentTime 141200 TM 6
[0008,0050] AccessionNumber I20160141126 SH 12
[0008,0060] Modality CT CS 2
[0008,0064] ConversionType WSD CS 4
[0008,0070] Manufacturer Philips LO 8
[0008,0080] InstitutionName InstitutionName LO 20
[0008,0081] InstitutionAddress InstitutionAddress ST 6
[0008,0090] ReferringPhysicianName ReferringPhysicianName PN 14
[0008,1010] StationName PHILIPS-705 SH 12
[0008,1030] StudyDescription CT Cardiac Angiography[3D] LO 26
[0008,1032] ProcedureCodeSequence SQ 92
[fffe,e000] Item na 76
[0008,0100] CodeValue 2CGC05CAD SH 10
[0008,0102] CodingSchemeDesignator GEIIS SH 6
[0008,0103] CodingSchemeVersion 0 SH 2
[0008,0104] CodeMeaning CT Cardiac Angiography[3D] LO 26
[0008,103e] SeriesDescription AXI 75% 74-66-68 LO 18
[0008,1040] InstitutionalDepartmentName Radiology LO 10
[0008,1070] OperatorsName HHH PN 4
[0008,1090] ManufacturerModelName Brilliance 64 LO 14
[0009,0000] PrivateGroupLength 14 UL 4
[0009,0010] PrivateCreator GEIIS LO 6
[0010,0010] PatientName PatientName PN 12
[0010,0020] PatientID PatientID LO 8
[0010,0021] IssuerOfPatientID WONJU CHRISTIAN HOSPITAL LO 24
[0010,0030] PatientBirthDate 19620218 DA 8
[0010,0040] PatientSex PatientSex CS 2
[0010,1010] PatientAge PatientAge AS 4
[0010,1040] PatientAddress ìía101- LO 12
[0018,0010] ContrastBolusAgent CONTRAST LO 8
[0018,0022] ScanOptions HELIX CS 6
[0018,0050] SliceThickness 0.550000017 DS 12
[0018,0060] KVP 120 DS 4
[0018,0090] DataCollectionDiameter 500 DS 4
[0018,1016] SecondaryCaptureDeviceManufacturer Philips LO 8
[0018,1018] SecondaryCaptureDeviceManufacturerModelName Brilliance64 LO 12
[0018,1019] SecondaryCaptureDeviceSoftwareVersions 3.5 LO 4
[0018,1020] SoftwareVersions 2.6.2 LO 6
[0018,1030] ProtocolName CARDIAC ANGIO/Cardiac LO 22
[0018,1100] ReconstructionDiameter 192 DS 4
[0018,1120] GantryDetectorTilt 0 DS 2
[0018,1130] TableHeight 85 DS 10
[0018,1140] RotationDirection CW CS 2
[0018,1150] ExposureTime 2100 IS 4
[0018,1151] XRayTubeCurrent 405 IS 4
[0018,1152] Exposure 850 IS 4
[0018,1160] FilterType XCC SH 4
[0018,1210] ConvolutionKernel XCC SH 4
[0018,5100] PatientPosition FFS CS 4
[0020,000d] StudyInstanceUID 1.2.840.113704.1.111.4756.1481519520.1 UI 38
[0020,000e] SeriesInstanceUID 1.2.840.113704.7.1.1.8088.1481523951.1 UI 38
[0020,0010] StudyID 125987 SH 6
[0020,0011] SeriesNumber 80688 IS 6
[0020,0012] AcquisitionNumber IS 0
[0020,0013] InstanceNumber 1 IS 2
[0020,0020] PatientOrientation CS 0
[0020,0032] ImagePositionPatient [3] -75, 30, 440.654903 DS 18
[0020,0037] ImageOrientationPatient [6] 1, 0, 0, 0, 1, 0 DS 12
[0020,1041] SliceLocation 0 DS 2
[0020,4000] ImageComments AXI 75% 74-66-68 LT 18
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0010] Rows 512 US 2
[0028,0011] Columns 512 US 2
[0028,0030] PixelSpacing [2] 0.375, 0.375 DS 12
[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 [2] 150, 150 DS 8
[0028,1051] WindowWidth [2] 900, 900 DS 8
[0028,1052] RescaleIntercept -1024 DS 6
[0028,1053] RescaleSlope 1 DS 2
[0032,1033] RequestingService CAR LO 4
[0040,0012] PreMedication LO 0
[0040,0253] PerformedProcedureStepID 12598756 SH 8
[0040,0254] PerformedProcedureStepDescription CT Cardiac Angiography[3D] LO 26
[0040,0275] RequestAttributesSequence SQ 36
[fffe,e000] Item na 20
[0040,1001] RequestedProcedureID I20160141126 SH 12
[0040,2017] FillerOrderNumberImagingServiceRequest RAD24 LO 6
[0040,3001] ConfidentialityConstraintOnPatientDataDescription LO 0
[0088,0200] IconImageSequence SQ 16498
[fffe,e000] Item na 16482
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0010] Rows 128 US 2
[0028,0011] Columns 128 US 2
[0028,0100] BitsAllocated 8 US 2
[0028,0101] BitsStored 8 US 2
[0028,0102] HighBit 7 US 2
[0028,0103] PixelRepresentation 0 US 2
[7fe0,0010] PixelData 0 OW 16384
[00e1,0010] PrivateCreator ELSCINT1 LO 8
[00e1,1014] Unknown N CS 2
[00e1,1022] Unknown [2] 0, 0 DS 4
[00e1,1023] Unknown [2] 1, 1 DS 4
[00e1,1040] OffsetFromCTMRImages AXI 75% 74-66-68 SH 18
[07a1,0010] PrivateCreator ELSCINT1 LO 8
[07a1,1010] Unknown Tag & Data 3.5 LO 4
[0903,0010] PrivateCreator GEIIS PACS LO 10
[0903,1010] Unknown Tag & Data 0 US 2
[0903,1011] Unknown Tag & Data 0 US 2
[0903,1012] Unknown Tag & Data 0 US 2
[0905,0010] PrivateCreator GEIIS LO 6
[0905,1030] Unknown Tag & Data WONJU CHRISTIAN HOSPITAL LO 24
[3109,0010] PrivateCreator Applicare/RadWorks/Version 5.0 LO 30
[3109,0011] PrivateCreator Applicare/RadWorks/Version 6.0/Summary LO 38
[3109,1002] Unknown Tag & Data NEW SH 4
[3109,1008] Unknown Tag & Data 192.168.1.176 LO 14
[3109,100a] Unknown Tag & Data 20170727 DA 8
[3109,100b] Unknown Tag & Data 203911 TM 6
[3109,1112] Unknown Tag & Data GEPACS ST 6
[7fd1,0000] PrivateGroupLength 26 UL 4
[7fd1,0010] PrivateCreator GEIIS LO 6
[7fd1,1010] Unknown Tag & Data 0 UL 4
[7fe0,0000] GenericGroupLength 524300 UL 4
[7fe0,0010] PixelData 0 OW 524288
Thank you for the information. I’ve added more metadata query capability to Slicer so that I can investigate your issue. Please install the latest nightly version of Slicer and follow these steps:
- Open DICOM browser
- Click on the patient
- Check
Advancedcheckbox - Click `Metadata button
- Enter
Imagein the search box - Click
Copy all files metadatabutton to copy image position information on the clipboard - Paste it to an empty Excel sheet
- Upload the Excel sheet to OneDrive, Dropbox, or any other file sharing service, and paste the link in your response (taking a screenshot of the sheet and attaching it is not enough, as only a small fraction of the data would be visible)
Sorry for late response.
Your latest nightly version 4.7.0 does not import any DICOM data.
After completing SlicerApp-real process,
DICOM Directory Import says
Directory import complete
0 new patients
0 new studies
0 new series
0 new instances
I think this is another bug. Please check it. Thanks
Please choose a writeable DICOM database directory (click on the double-arrow icon next to the Repair menu item at the top to see the directory selector) and then import the images again. If import fails then copy-paste the application log here (menu: File / Report a bug).
It happens when you first instal the software. Try to restart your computer and try again. It should work.
Best Regards,
Rasha