Can't load dicom images generated by dcmtk

Support
1

Hi,
I have generated few dicom using dcmtk. I can open them using some software (imagej, xnview etc …).
dcm2pnm test0004.dcm test.bmp works perfectly, as well as dcmdump G:\Contracts\Novartis\test0004.dcm
so the dicom file must not be far from something “good”.
output of dcmdump:

DICOM tags 
# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 198                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI [1.2.276.0.7230010.3.1.0.1]              #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.276.0.7230010.3.1.4.613533732.15860.1561626548.497] #  54, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit                    #  20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.4]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_364]                        #  16, 1 ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0005) CS [ISO_IR 100]                             #  10, 1 SpecificCharacterSet
(0008,0020) DA [20190627]                               #   8, 1 StudyDate
(0008,0021) DA [20190627]                               #   8, 1 SeriesDate
(0008,0022) DA [20190627]                               #   8, 1 AcquisitionDate
(0008,0023) DA [20190627]                               #   8, 1 ContentDate
(0008,0030) TM [110908.000]                             #  10, 1 StudyTime
(0008,0031) TM [110908.000]                             #  10, 1 SeriesTime
(0008,0032) TM [110908.000]                             #  10, 1 AcquisitionTime
(0008,0033) TM [110908.000]                             #  10, 1 ContentTime
(0008,0060) CS [OCT]                                    #   4, 1 Modality
(0008,0070) LO [Heidelberg Engineering]                 #  22, 1 Manufacturer
(0008,0090) PN (no value available)                     #   0, 0 ReferringPhysicianName
(0008,0221) CS [OCT]                                    #   4, 1 EquipmentModality
(0008,103e) LO [OCT]                                    #   4, 1 SeriesDescription
(0008,1070) PN [GYS]                                    #   4, 1 OperatorsName
(0008,1090) LO [Spectralis]                             #  10, 1 ManufacturerModelName
(0010,0020) LO [1.4.444.0.1.4.613533732.15860.1561626542.494] #  44, 1 PatientID
(0010,0040) CS [F]                                      #   2, 1 PatientSex
(0018,0050) DS [0.0598645833333333]                     #  18, 1 SliceThickness
(0020,000d) UI [1.4.444.0.1.2.613533732.15860.1561626542.495] #  44, 1 StudyInstanceUID
(0020,000e) UI [1.4.444.0.1.3.613533732.15860.1561626542.496] #  44, 1 SeriesInstanceUID
(0020,0010) SH [test]                                   #   4, 1 StudyID
(0020,0011) IS [0]                                      #   2, 1 SeriesNumber
(0020,0060) CS [OS]                                     #   2, 1 Laterality
(0020,1041) DS [0.0598645833333333]                     #  18, 1 SliceLocation
(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 496                                      #   2, 1 Rows
(0028,0011) US 1024                                     #   2, 1 Columns
(0028,0030) DS [0.0057\0.0039]                          #  14, 2 PixelSpacing
(0028,0100) US 8                                        #   2, 1 BitsAllocated
(0028,0101) US 8                                        #   2, 1 BitsStored
(0028,0102) US 7                                        #   2, 1 HighBit
(0028,0103) US 0                                        #   2, 1 PixelRepresentation
(7fe0,0010) OB 00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00... # 507904, 1 PixelData

but I can not open them using Slicer. I give me this error:
“Exception thrown in event: Calling methods on uninitialized ctkDICOMItem”

2

Technically, this is not a valid DICOM image as it is missing Type 1 fields. Specifically, type 1 tags Image Orientation Patient (0020,0037), Image Position Patient (0020,0032). I suspect viewers that treat this as a simple bitmap may find this acceptable, but tools that want are interested in spatial position will find this underspecified.

1 Like
3

thanks for the answer, I was suspecting something like that, even if in eye oct ( Ophthalmic Optical Coherence Tomography B-scan Volume Analysis CIOD : https://dicom.innolitics.com/ciods/ophthalmic-optical-coherence-tomography-b-scan-volume-analysis) it does not make much sens, they are not even in the list of fields for this type of images on this website. I will try to add these fields with “random values”

4

I see that the frame of reference is “requested” as well but don’t get what it refers to. I have some ct scan, for which there is an uid in this field 0020,0052 but the uid in it doesn’t match with any uid in the studies.

5

If OCT images do not require these fields then the proper solution would be to add a DICOM plugin to handle these volumes. You can write a DICOM import plugin by cloning an existing plugin and customizing it. See for example scalar volume importer plugin here and some ultrasound importer plugins here.

You may also use DICOM Patcher module to add image plane fields (image position patient, image orientation patient, etc.).

6

Frame of reference UID is usually the same across series in a study. But I am sure there can be exceptions, and in any case Slicer is not using it, so if you don’t have it, it’s not a problem for loading images into Slicer.

7

thanks. I have added an empty value just in case

8

thanks to you, I have added the missing field an now it loads the dicom but not correctly.
SlicerError3
it sees there is 97 dicom files and load all of them.
Slicer
SlicerError2
all slices have the same image.
and normally on the “view metadata interface”, there is the possibility to navigate between instance of the same series with a slider, which I don’t have.
(I have checked using dcm2pnm the image is different each time, the problem doesn’t come from there).

here are 3 dcmdump as example.
the image position and instance number change for each “slice”. so I don’t get why it displays always the same slice.

test0030.dcm 
# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 186                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage            #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit                    #  20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.4]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_364]                        #  16, 1 ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0005) CS [ISO_IR 100]                             #  10, 1 SpecificCharacterSet
(0008,0016) UI =SecondaryCaptureImageStorage            #  26, 1 SOPClassUID
(0008,0018) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 SOPInstanceUID
(0008,0020) DA [20190628]                               #   8, 1 StudyDate
(0008,0021) DA [20190628]                               #   8, 1 SeriesDate
(0008,0022) DA [20190628]                               #   8, 1 AcquisitionDate
(0008,0023) DA [20190628]                               #   8, 1 ContentDate
(0008,0030) TM [092450.000]                             #  10, 1 StudyTime
(0008,0031) TM [092450.000]                             #  10, 1 SeriesTime
(0008,0032) TM [092450.000]                             #  10, 1 AcquisitionTime
(0008,0033) TM [092450.000]                             #  10, 1 ContentTime
(0008,0050) SH (no value available)                     #   0, 0 AccessionNumber
(0008,0060) CS [OCT]                                    #   4, 1 Modality
(0008,0070) LO [Heidelberg Engineering]                 #  22, 1 Manufacturer
(0008,0090) PN (no value available)                     #   0, 0 ReferringPhysicianName
(0008,0221) CS [OCT]                                    #   4, 1 EquipmentModality
(0008,103e) LO [OCT]                                    #   4, 1 SeriesDescription
(0008,1070) PN [GYS]                                    #   4, 1 OperatorsName
(0008,1090) LO [Spectralis]                             #  10, 1 ManufacturerModelName
(0010,0010) PN (no value available)                     #   0, 0 PatientName
(0010,0020) LO [1.4.444.0.1.4.613533732.156.1561706684.738] #  42, 1 PatientID
(0010,0040) CS [F]                                      #   2, 1 PatientSex
(0010,1010) AS (no value available)                     #   0, 0 PatientAge
(0018,0050) DS [0.0598645833333333]                     #  18, 1 SliceThickness
(0018,5100) CS [HFP]                                    #   4, 1 PatientPosition
(0020,000d) UI [1.4.444.0.1.2.613533732.156.1561706684.740] #  42, 1 StudyInstanceUID
(0020,000e) UI [1.4.444.0.1.3.613533732.156.1561706684.741] #  42, 1 SeriesInstanceUID
(0020,0010) SH [test]                                   #   4, 1 StudyID
(0020,0011) IS [1]                                      #   2, 1 SeriesNumber
(0020,0013) IS [31]                                     #   2, 1 InstanceNumber
(0020,0032) DS [0\0\1.85580208333333]                   #  20, 3 ImagePositionPatient
(0020,0037) DS [1\0\0\0\1\0]                            #  12, 6 ImageOrientationPatient
(0020,0060) CS [L]                                      #   2, 1 Laterality
(0020,1041) DS [1.85580208333333]                       #  16, 1 SliceLocation
(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 496                                      #   2, 1 Rows
(0028,0011) US 1024                                     #   2, 1 Columns
(0028,0030) DS [0.0057\0.0039]                          #  14, 2 PixelSpacing
(0028,0100) US 8                                        #   2, 1 BitsAllocated
(0028,0101) US 8                                        #   2, 1 BitsStored
(0028,0102) US 7                                        #   2, 1 HighBit
(0028,0103) US 0                                        #   2, 1 PixelRepresentation
(7fe0,0010) OB 00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00... # 507904, 1 PixelData
test0010.dcm 
# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 186                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage            #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit                    #  20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.4]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_364]                        #  16, 1 ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0005) CS [ISO_IR 100]                             #  10, 1 SpecificCharacterSet
(0008,0016) UI =SecondaryCaptureImageStorage            #  26, 1 SOPClassUID
(0008,0018) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 SOPInstanceUID
(0008,0020) DA [20190628]                               #   8, 1 StudyDate
(0008,0021) DA [20190628]                               #   8, 1 SeriesDate
(0008,0022) DA [20190628]                               #   8, 1 AcquisitionDate
(0008,0023) DA [20190628]                               #   8, 1 ContentDate
(0008,0030) TM [092450.000]                             #  10, 1 StudyTime
(0008,0031) TM [092450.000]                             #  10, 1 SeriesTime
(0008,0032) TM [092450.000]                             #  10, 1 AcquisitionTime
(0008,0033) TM [092450.000]                             #  10, 1 ContentTime
(0008,0050) SH (no value available)                     #   0, 0 AccessionNumber
(0008,0060) CS [OCT]                                    #   4, 1 Modality
(0008,0070) LO [Heidelberg Engineering]                 #  22, 1 Manufacturer
(0008,0090) PN (no value available)                     #   0, 0 ReferringPhysicianName
(0008,0221) CS [OCT]                                    #   4, 1 EquipmentModality
(0008,103e) LO [OCT]                                    #   4, 1 SeriesDescription
(0008,1070) PN [GYS]                                    #   4, 1 OperatorsName
(0008,1090) LO [Spectralis]                             #  10, 1 ManufacturerModelName
(0010,0010) PN (no value available)                     #   0, 0 PatientName
(0010,0020) LO [1.4.444.0.1.4.613533732.156.1561706684.738] #  42, 1 PatientID
(0010,0040) CS [F]                                      #   2, 1 PatientSex
(0010,1010) AS (no value available)                     #   0, 0 PatientAge
(0018,0050) DS [0.0598645833333333]                     #  18, 1 SliceThickness
(0018,5100) CS [HFP]                                    #   4, 1 PatientPosition
(0020,000d) UI [1.4.444.0.1.2.613533732.156.1561706684.740] #  42, 1 StudyInstanceUID
(0020,000e) UI [1.4.444.0.1.3.613533732.156.1561706684.741] #  42, 1 SeriesInstanceUID
(0020,0010) SH [test]                                   #   4, 1 StudyID
(0020,0011) IS [1]                                      #   2, 1 SeriesNumber
(0020,0013) IS [11]                                     #   2, 1 InstanceNumber
(0020,0032) DS [0\0\0.658510416666667]                  #  22, 3 ImagePositionPatient
(0020,0037) DS [1\0\0\0\1\0]                            #  12, 6 ImageOrientationPatient
(0020,0060) CS [L]                                      #   2, 1 Laterality
(0020,1041) DS [0.658510416666667]                      #  18, 1 SliceLocation
(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 496                                      #   2, 1 Rows
(0028,0011) US 1024                                     #   2, 1 Columns
(0028,0030) DS [0.0057\0.0039]                          #  14, 2 PixelSpacing
(0028,0100) US 8                                        #   2, 1 BitsAllocated
(0028,0101) US 8                                        #   2, 1 BitsStored
(0028,0102) US 7                                        #   2, 1 HighBit
(0028,0103) US 0                                        #   2, 1 PixelRepresentation
(7fe0,0010) OB 00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00... # 507904, 1 PixelData
test0020.dcm 
# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 186                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage            #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit                    #  20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.4]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_364]                        #  16, 1 ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Explicit
(0008,0005) CS [ISO_IR 100]                             #  10, 1 SpecificCharacterSet
(0008,0016) UI =SecondaryCaptureImageStorage            #  26, 1 SOPClassUID
(0008,0018) UI [1.4.444.0.1.4.613533732.156.1561706684.739] #  42, 1 SOPInstanceUID
(0008,0020) DA [20190628]                               #   8, 1 StudyDate
(0008,0021) DA [20190628]                               #   8, 1 SeriesDate
(0008,0022) DA [20190628]                               #   8, 1 AcquisitionDate
(0008,0023) DA [20190628]                               #   8, 1 ContentDate
(0008,0030) TM [092450.000]                             #  10, 1 StudyTime
(0008,0031) TM [092450.000]                             #  10, 1 SeriesTime
(0008,0032) TM [092450.000]                             #  10, 1 AcquisitionTime
(0008,0033) TM [092450.000]                             #  10, 1 ContentTime
(0008,0050) SH (no value available)                     #   0, 0 AccessionNumber
(0008,0060) CS [OCT]                                    #   4, 1 Modality
(0008,0070) LO [Heidelberg Engineering]                 #  22, 1 Manufacturer
(0008,0090) PN (no value available)                     #   0, 0 ReferringPhysicianName
(0008,0221) CS [OCT]                                    #   4, 1 EquipmentModality
(0008,103e) LO [OCT]                                    #   4, 1 SeriesDescription
(0008,1070) PN [GYS]                                    #   4, 1 OperatorsName
(0008,1090) LO [Spectralis]                             #  10, 1 ManufacturerModelName
(0010,0010) PN (no value available)                     #   0, 0 PatientName
(0010,0020) LO [1.4.444.0.1.4.613533732.156.1561706684.738] #  42, 1 PatientID
(0010,0040) CS [F]                                      #   2, 1 PatientSex
(0010,1010) AS (no value available)                     #   0, 0 PatientAge
(0018,0050) DS [0.0598645833333333]                     #  18, 1 SliceThickness
(0018,5100) CS [HFP]                                    #   4, 1 PatientPosition
(0020,000d) UI [1.4.444.0.1.2.613533732.156.1561706684.740] #  42, 1 StudyInstanceUID
(0020,000e) UI [1.4.444.0.1.3.613533732.156.1561706684.741] #  42, 1 SeriesInstanceUID
(0020,0010) SH [test]                                   #   4, 1 StudyID
(0020,0011) IS [1]                                      #   2, 1 SeriesNumber
**(0020,0013) IS [21]                                     #   2, 1 InstanceNumber**
**(0020,0032) DS [0\0\1.25715625]                         #  14, 3 ImagePositionPatient**
**(0020,0037) DS [1\0\0\0\1\0]                            #  12, 6 ImageOrientationPatient**
(0020,0060) CS [L]                                      #   2, 1 Laterality
(0020,1041) DS [1.25715625]                             #  10, 1 SliceLocation
(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 496                                      #   2, 1 Rows
(0028,0011) US 1024                                     #   2, 1 Columns
(0028,0030) DS [0.0057\0.0039]                          #  14, 2 PixelSpacing
(0028,0100) US 8                                        #   2, 1 BitsAllocated
(0028,0101) US 8                                        #   2, 1 BitsStored
(0028,0102) US 7                                        #   2, 1 HighBit
(0028,0103) US 0                                        #   2, 1 PixelRepresentation
(7fe0,0010) OB 00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00... # 507904, 1 PixelData

on the python console it shows this:

Irregular volume geometry detected (maximum error of 1020.01 mm is above tolerance threshold of 0.001 mm).  Regularization transform is not added, as the option is disabled.

and apparently it uses the dicomscalarvolumplugin to open it.
but I don’t know how to put breakpoint in it to see what happens.

9

I just tried with adding a different acquisition time and content time for each slices, but I have got the same result. it shows only one slice, in the display and in the metadata viewer.

10

@pdeman - it seems like a converter to make 3D volumes from your data could be a useful bit of code - would you be able to make it an open source tool along with some examples? If so it would be a lot easier for us to help you debug.

11

The metadata is still invalid, as the same SOP instance UID is reused in multiple files. This UID must be unique in each file.

You do not need to use different acquisition or content time. If you do, then you have the option of loading only group of frames that have the same acquisition or content time (if you enable “Allow loading subseries by time” in Application settings / DICOM).

12

ok thanks, I did the correction and it works now. except that when I change slices, it says they are 1 mm spaced, instead of 0.059 mm

13

Slice thickness field is not intended for defining geometry (such as distance between slices). Instead, slice spacing is defined by “image position patient” tag (position of next slice is obtained by incrementing previous slice position by slice spacing).

14

I still have a problem with the geometry that I don’t get.
the problem seems to come from:
sliceCornersFromIJKToRAS in DICOMScalarVolumePlugin.py

  volumeNode.GetIJKToRASMatrix(ijkToRAS)
  print(ijkToRAS)

return:

Loading with imageIOName: GDCM
vtkMatrix4x4 (000001FC74D84AD0)
Debug: Off
Modified Time: 323439
Reference Count: 1
Registered Events: (none)
Elements:
-1 0 0 0
0 -1 0 0
0 0 1 0
0 0 0 1

so the self.originalCorners are matrix in “pixel”
while self.targetCorners
read from the dicom header in this python script are correct.

how the matrix GetIJKToRASMatrix is initialized ? why in my case it is incorrect ?

15

What is your problem? Image loaded but spacing is 1.0?

Are any error messages logged?

Could you send a sample data set?

16

yes all spacing (in the 3 directions) is 1.0.
I get a warning :slight_smile:

if maxError > self.cornerEpsilon:
warningText = “Irregular volume geometry detected (maximum error of %g mm is above tolerance threshold of %g mm).” % (maxError, self.cornerEpsilon)

and maxError is high due to the fact that self.originalCorners does’nt take into account the spacing.

here is a dcmdump:

Dicom-File-Format

Dicom-Meta-Information-Header

Used TransferSyntax: Little Endian Explicit

(0002,0000) UL 188 # 4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion
(0002,0002) UI =SecondaryCaptureImageStorage # 26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.4.444.0.1.4.560454010.10948.1568207717.271] # 44, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit # 20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.4] # 28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_364] # 16, 1 ImplementationVersionName

Dicom-Data-Set

Used TransferSyntax: Little Endian Explicit

(0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
(0008,0016) UI =SecondaryCaptureImageStorage # 26, 1 SOPClassUID
(0008,0018) UI [1.4.444.0.1.4.560454010.10948.1568207717.271] # 44, 1 SOPInstanceUID
(0008,0020) DA [20151214] # 8, 1 StudyDate
(0008,0021) DA [20151214] # 8, 1 SeriesDate
(0008,0022) DA [20151214] # 8, 1 AcquisitionDate
(0008,0023) DA [20151214] # 8, 1 ContentDate
(0008,0030) TM [000000.0000] # 12, 1 StudyTime
(0008,0031) TM [000000.0000] # 12, 1 SeriesTime
(0008,0032) TM [180136.136] # 10, 1 AcquisitionTime
(0008,0033) TM [180136.136] # 10, 1 ContentTime
(0008,0050) SH (no value available) # 0, 0 AccessionNumber
(0008,0060) CS [OPT] # 4, 1 Modality
(0008,0070) LO [xxx] # 22, 1 Manufacturer
(0008,0090) PN (no value available) # 0, 0 ReferringPhysicianName
(0008,0221) CS [OCT] # 4, 1 EquipmentModality
(0008,103e) LO [SlicesOPT] # 10, 1 SeriesDescription
(0008,1070) PN [GYS] # 4, 1 OperatorsName
(0008,1090) LO [Spectralis] # 10, 1 ManufacturerModelName
(0010,0010) PN [visit x] # 30, 1 PatientName
(0010,0020) LO [LOC6053359.1.3.6.1.4.1.33437.10.7.2548426.13094654189.13010.7] # 62, 1 PatientID
(0010,0030) DA [19000101] # 8, 1 PatientBirthDate
(0010,0040) CS [F] # 2, 1 PatientSex
(0010,1010) AS (no value available) # 0, 0 PatientAge
(0018,0050) DS [0.0598645833333333] # 18, 1 SliceThickness
(0018,5100) CS [HFP] # 4, 1 PatientPosition
(0020,000d) UI [LOC13309808.1.3.6.1.4.1.33437.10.8.2673601.13094590126.7801.8] # 62, 1 StudyInstanceUID
(0020,000e) UI [LOC13309808.1.3.6.1.4.1.33437.10.9.2673601.13094590127.7801.9] # 62, 1 SeriesInstanceUID
(0020,0010) SH # 12, 1 StudyID
(0020,0011) IS [1] # 2, 1 SeriesNumber
(0020,0013) IS [15] # 2, 1 InstanceNumber
(0020,0032) DS [0\0\0.89796875] # 14, 3 ImagePositionPatient
(0020,0037) DS [1\0\0\0\1\0] # 12, 6 ImageOrientationPatient
(0020,0052) UI [1.4.444.0.1.3.560454010.10948.1568207717.256] # 44, 1 FrameOfReferenceUID
(0020,0060) CS [L] # 2, 1 Laterality
(0020,1041) DS [0.89796875] # 10, 1 SliceLocation
(0028,0002) US 1 # 2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation
(0028,0008) IS [1] # 2, 1 NumberOfFrames
(0028,0010) US 496 # 2, 1 Rows
(0028,0011) US 1024 # 2, 1 Columns
(0028,0030) DS [0.0057\0.0039] # 14, 2 PixelSpacing
(0028,0100) US 8 # 2, 1 BitsAllocated
(0028,0101) US 8 # 2, 1 BitsStored
(0028,0102) US 7 # 2, 1 HighBit
(0028,0103) US 0 # 2, 1 PixelRepresentation
(7fe0,0010) OB 00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00… # 507904, 1 PixelData

I’ll upload some data soon.

17

I can’t upload .dcm on the forum

18

When the data is a secondary capture it basically means screenshot, which isn’t really a volumetric format.

You can use dropbox, google drive, one drive, etc to share the data.

19

yes but it doesn’t work with opthalmic tomographic uid neither, even if they are volumetric format.
so indeed if I specify for example a CTImageStorage sop class uid, it works.
but it’s not a CTImageStorage …
how can I know which sop class uid are managed by slicer ?

20

There is no restriction in term of SOP Class UID, but Slicer’s Scalar volume DICOM reader plugin requires image geometry information defined by slice position and orientation tags.

If ophtalmic tomographic image IOD does not require these fields then you need to create your own DICOM plugin for reading this type of image. A plugin would probably be just a few ten lines of Python code that computes image origin, spacing, and axis directions from DICOM tags - see my post above for details.