Hello!
I am using 3D Slicer in order to measure certain vertical measurements and angular measurements of the mandible. I am noticing that the millimeter measurements are not giving me the correct measurement. For example, a measurement that should be reading 65mm (vertical height of the ramus), is giving me 185mm in 3D Slicer. Is there a solution to this problem? Is there some sort of way to calibrate the 3D Slicer ruler based on the original CBCT scan information?
If you go to the Volumes module and open Volume Information you can check the spacing values. Are they as expected?
Thank you for your prompt response!
My initial CBCT scan files were exported from Dolphin 3D. I first sculpted
the body of the mandible out, in order to obtain more accurate
measurements. Then I exported the DICOM file of the sculpted mandible, from
Dolphin 3D, and opened the file in 3D Slicer.
After this was done, I went into the Volumes module of 3D Slicer, to adjust
the spacing values and origin values.
For more clarification, I have attached a screenshot to this email. On the
right, is 3D Slicer with the Volume Information available to be adjusted.
On the left, is Dolphin 3D with the original values of the CBCT scan.
Do the numbers listed for ‘Image Spacing’ and ‘Image Origin’ in 3D Slicer
make sense, given the original values in Dolphin 3D?
Peyton
Volume Size (Voxels) = Image Dimensions in Slicer
Voxel Size (mm^3) = Image Spacing in Slicer
Dolphin 3D does not show position of image origin.
How did you export the volume from Dolphin 3D? What file format did you export to? Were there any options for the export?
Thank you for your prompt response, and your help! My apologies for the
delay.
I have attached a screen shot of the method I use to export the file. I
choose to export the file at ‘1:1 No Loss/Uncompressed’, and I export it as
a single DICOM file. I save the file to a local folder, and then upload
that file directly to the 3D Slicer software. There are various options to
save the file, which can be seen in the attachment. There are also other
options for compression, which I do not choose.
Peyton
Could you please send us the DICOM metadata of the image? See instructions here: https://www.slicer.org/wiki/Documentation/Nightly/Modules/DICOM#How_to_obtain_DICOM_metadata
For some reason, the “Copy Metadata” button was not listed.
I have taken a screenshot of the window that appears in order for me to
obtain the Metadata for the scan.
Is there a way for me to copy the metadata, that I am not seeing?
[image deleted]
I have attached a better screenshot to this email.
My apologies!
Peyton
[Image deleted]
Hi - could you use the anonymize option when exporting from Dolphin and the latest version of Slicer (4.8) to get access to the option for copying metadata.
Thanks
Thank you again for those specific instructions! I was able to get access
to copying the metadata.
Hope to hear from you all soon!
[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType [2] DERIVED, PRIMARY CS 16
[0008,0012] InstanceCreationDate 20171130 DA 8
[0008,0013] InstanceCreationTime 120140.0 TM 8
[0008,0014] InstanceCreatorUID 99999 UI 6
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.2 UI 26
[0008,0018] SOPInstanceUID
2.16.840.1.114363.0999.000.1.1.1512064900.0.123380.23376.28.1 UI 62
[0008,0020] StudyDate 20171130 DA 8
[0008,0021] SeriesDate 20171130 DA 8
[0008,0022] AcquisitionDate 20171130 DA 8
[0008,0023] ContentDate 20171130 DA 8
[0008,0030] StudyTime 120140.0 TM 8
[0008,0031] SeriesTime 120140.0 TM 8
[0008,0032] AcquisitionTime 175436 TM 6
[0008,0033] ContentTime 120140.0 TM 8
[0008,0050] AccessionNumber SH 0
[0008,0060] Modality CT CS 2
[0008,0070] Manufacturer Imaging Sciences International LO 30
[0008,0080] InstitutionName Sellke and Reily Ortho LO 22
[0008,0081] InstitutionAddress 30 North Slusser Street
Suite 1
Grayslake, IL 60030 ST 52
[0008,0090] ReferringPhysicianName PN 0
[0008,1010] StationName I-CAT SH 6
[0008,103e] SeriesDescription Dolphin3D Internal LO 18
[0008,1050] PerformingPhysicianName PN 0
[0008,1070] OperatorsName ortho PN 6
[0008,1090] ManufacturerModelName 17-19 LO 6
[0009,0100] Unknown Tag & Data 11753 LO 6
[0009,0101] Unknown Tag & Data 1 IS 2
[0010,0010] PatientName Anonymous Anonymous PN 20
[0010,0020] PatientID Anonymous LO 10
[0010,0030] PatientBirthDate 20000101 DA 8
[0010,0040] PatientSex M CS 2
[0010,2160] EthnicGroup SH 0
[0010,4000] PatientComments LT 0
[0018,0022] ScanOptions LANDSCAPE CS 10
[0018,0050] SliceThickness 0.399998009204865 DS 18
[0018,0060] KVP 120 DS 4
[0018,0090] DataCollectionDiameter 130.00 DS 6
[0018,1000] DeviceSerialNumber ICU-080677 LO 10
[0018,1020] SoftwareVersions 1.9.3.13 LO 8
[0018,1150] ExposureTime 4 IS 2
[0018,1151] XRayTubeCurrent 5 IS 2
[0018,5100] PatientPosition CS 0
[0019,1000] Unknown Tag & Data ISI_ACQU_1 LO 10
[0019,1043] Unknown Tag & Data 1 IS 2
[0019,1050] Unknown Tag & Data 55.4864848409 DS 14
[0019,1051] Unknown Tag & Data 42.0000000000 DS 14
[0019,2000] Unknown Tag & Data LO 0
[0019,2001] Unknown Tag & Data lVCVRGUmP71OnVPQKhMWnTlcQQ0 LO 28
[0020,000d] StudyInstanceUID
2.16.840.1.114363.0999.000.1.1.1512064900.0.123548.25381.13260.2 UI 64
[0020,000e] SeriesInstanceUID
2.16.840.1.114363.0999.000.1.1.1512064900.0.123548.1950.21266.29 UI 64
[0020,0010] StudyID 1 SH 2
[0020,0011] SeriesNumber 1 IS 2
[0020,0012] AcquisitionNumber 164 IS 4
[0020,0013] InstanceNumber 1 IS 2
[0020,0032] ImagePositionPatient [3] -200, -200, -30.7999992370605 DS 28
[0020,0037] ImageOrientationPatient [6] 1.000000, 0.000000, 0.000000,
0.000000, 1.000000, 0.000000 DS 54
[0020,0052] FrameOfReferenceUID
2.16.840.114421.80677.9451500894.9483036894 UI 44
[0020,1040] PositionReferenceIndicator LO 0
[0020,1041] SliceLocation -30.7999992370605 DS 18
[0021,1032] Unknown Tag & Data 18.537371 DS 10
[0021,1034] Unknown Tag & Data 8.883619 DS 8
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0008] NumberOfFrames 256 IS 4
[0028,0010] Rows 291 US 2
[0028,0011] Columns 387 US 2
[0028,0030] PixelSpacing [2] 0.400000005960464, 0.400000005960464 DS 36
[0028,0100] BitsAllocated 16 US 2
[0028,0101] BitsStored 16 US 2
[0028,0102] HighBit 15 US 2
[0028,0103] PixelRepresentation 0 US 2
[0028,0106] SmallestImagePixelValue 0 US 2
[0028,0107] LargestImagePixelValue 65535 US 2
[0028,1050] WindowCenter 600 DS 4
[0028,1051] WindowWidth 3200 DS 4
[0028,1052] RescaleIntercept -1000 DS 6
[0028,1053] RescaleSlope 1 DS 2
[0032,4000] RETIRED_StudyComments LT 0
[7fe0,0010] PixelData 0000 OW 57659904
[aaa1,2020] Unknown Tag & Data 0 0 0 0 30 72 SH 14
I just remember that we have added a some rules to the DICOM Patcher module that fixes these Dolphin3D-exported files (they are not conform to the DICOM standard). Please run the DICOM Patcher module on your data set and then import it into Slicer. Voxel sizes in these patched DICOM files should be correct.
If you have a support contract with Dolphin3D manufacturer then you may let them know that their DICOM-exported files are invalid and they may contact us for details on how to fix their exporter.
Thank you so much for the suggestion!
I did run the DICOM Patcher Module for the scan, which did correct the
voxel discrepancy.
I’m still having the issue with the ruler calibration though.
I have attached screenshots of the issue, and the metadata.
These fields specify voxel size (image spacing):
[0018,0050] SliceThickness 0.399998009204865 DS 18
[0028,0030] PixelSpacing [2] 0.400000005960464, 0.400000005960464 DS 36
Can you check what image spacing values do you see in Volumes module? (they should be 0.4 0.4 0.4)
Hi I am wanting to calibrate the ruler for measurements of teeth as it is incorrect, is there a way I can do this? thank you in advance 
As the prior discussion indicates, Slicer simply uses the image spacing provided by your dataset. Did you import the data from DICOM series? If so, try running the dicom patcher as indicated.