Reading Dicom sequence data with SimpleITK

jonasteuwen · March 28, 2020, 4:20pm

When reading mammography images there are several Dicom tags relevant to be able to display the image correctly as described in the dicom standard. These are stored in the VOILUTFunction and VOILUTSequence. The first is a low-level tag, and can be easily read, however, the second does not.

For instance, dcmdump gives this for my file:

(base) ➜  pngs dcmdump mammogram.dcm | grep -i lut
(0028,1055) LO [linear LUT]                             #  10, 1 WindowCenterWidthExplanation
(0028,3010) SQ (Sequence with explicit length #=4)      # 32974, 1 VOILUTSequence
    (0028,3002) US 4096\0\12                                #   6, 3 LUTDescriptor
    (0028,3003) LO [Flavor3_35_280]                         #  14, 1 LUTExplanation
    (0028,3006) US 0\6\6\6\6\6\6\6\6\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7\7... # 8192,4096 LUTData
    (0028,3002) US 4096\0\12                                #   6, 3 LUTDescriptor
    (0028,3003) LO [Flavor3_37_250]                         #  14, 1 LUTExplanation
    (0028,3006) US 0\10\10\10\10\10\10\10\10\10\10\10\10\10\10\10\11\11\11\11\11\11\11... # 8192,4096 LUTData
    (0028,3002) US 4096\0\12                                #   6, 3 LUTDescriptor
    (0028,3003) LO [Flavor3_37_230]                         #  14, 1 LUTExplanation
    (0028,3006) US 0\11\11\11\11\11\11\11\11\11\12\12\12\12\12\12\12\12\12\12\12\12\12... # 8192,4096 LUTData
    (0028,3002) US 4096\0\12                                #   6, 3 LUTDescriptor
    (0028,3003) LO [Flavor3_LUT1]                           #  12, 1 LUTExplanation
    (0028,3006) US 0\17\17\17\17\17\18\18\18\18\18\18\18\18\18\18\18\18\18\18\18\18\19... # 8192,4096 LUTData

While with SimpleITK I get:

sitk_image.GetMetaData('0028|3010')

RuntimeError: Exception thrown in SimpleITK Image_GetMetaData: /Users/runner/runners/2.160.0/work/1/sitk-build/ITK/Modules/Core/Common/src/itkMetaDataDictionary.cxx:88:
itk::ERROR: Key '0028|3010' does not exist

Is there a way of doing this currently with SimpleITK or would it be better to use pydicom for this? It would be a little bit unfortunate, as this would mean I need to read the header twice (and have another dependency).

flaviu2 · March 28, 2020, 6:05pm

Seem that itkMetaDataDictionary class doesn’t know that tag, so an overcome will be to read that tag before SimpleITK with other lib/object, either to delete that tag, or, modify it, and consider later as you needs.

If you app allow to read the data with VTK, I can help you.

zivy · March 28, 2020, 7:11pm

Hello @jonasteuwen,

Generally speaking SimpleITK will read all the tags and they should be accessible.
How are you reading the images, ImageFileReader or ImageSeriesReader? Are all other tags loaded (GetMetaDataKeys)?

Possibly if you could share the code used for reading and the image we could better help you (preferably both, but just the code would help in understanding what went wrong).

jonasteuwen · March 28, 2020, 8:02pm

Hi @zivy

I am reading the image as follows (mammograms are single dicom files): img = sitk.ReadImage(fn). Other DICOM tags are properly read, and are in GetMetaDataKeys, however '0028|3010' is not. For instance, the modality tag img.GetMetaData('0008|0060') properly returns MG.

For instance this piece of code (with ImageFileReader) also does not output the sequence tags:

reader = sitk.ImageFileReader()

reader.SetFileName(image_fn)
reader.LoadPrivateTagsOn();

reader.ReadImageInformation();

for k in reader.GetMetaDataKeys():
    v = reader.GetMetaData(k)
    print(k, v)

Best,
Jonas

zivy · March 28, 2020, 9:34pm

Hi @jonasteuwen,

Code looks good, so it may be an issue with SimpleITK/ITK, possibly related to this question. Underneath the SimpleITK hood we are using GDCM, which does have a Python binding (Examples here).

If you can share the data we may be able to debug this or identify if we have missing functionality.

jonasteuwen · March 29, 2020, 11:13am

Dear @zivy, in that case I think it is a missing feature. I will see if I can find data which can be shared with such sequence information. Likely the same issue will arise with a CT scan with an associated RTSTRUCT.

Best,
Jonas.

blowekamp · March 29, 2020, 1:10pm

Hello,

What version of SimpleITK are you using? It may be worth trying SimpleITK 2.0 rc 1, as GDCM version has been updated which might address the issue.

jonasteuwen · April 13, 2020, 1:37pm

Hello Bradley,

I can confirm the problem still persists, I am only able to access the top-level keys tags, and no childs (which definitely exist if I check the output of dcmdump). I am not very familiar with the ITK source code, but if you could point me to the relevant part of the Metadata reading of DICOM images, I might be able to find the reason.

Best,
Jonas

blowekamp · April 13, 2020, 3:07pm

Hello,

SimpleITK used GDCM for reading the DICOM files and metadata. You can find the library on GitHub here:

The ITK class which interfaces with GDCM is here:

github.com

InsightSoftwareConsortium/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx

/*=========================================================================
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 *  you may not use this file except in compliance with the License.
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 *
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 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
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/*=========================================================================
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 *  Portions of this file are subject to the VTK Toolkit Version 3 copyright.

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@mathieu.malaterre is the maintainer of GDCM. I believe there should be some GDCM tools to inspect you file to verify if GDCM is doing the right thing, of if there is a problem with ITKGDCMImageIO.

mihail.isakov · April 13, 2020, 4:01pm

ITKGDCMImageIO doesn’t read sequences for metadata dictionary, s. here and here. It was never supported and already mentioned several times, e.g. the topic.

jonasteuwen · April 13, 2020, 8:27pm

Hi,

Thanks for figuring out where this is located. Is this a intended feature for ITK (I suppose that the sequences load slower) or would it be possible to allow to load this, e.g. with LoadDicomSequences() just as with LoadPrivateTags()? It seems more important than the private tags - imagine you want to match an RTSTRUCT with its CT scan. The ReferenceFrameUID is part of a sequence.

The DCMTK backend seems to support sequences.

mihail.isakov · April 14, 2020, 4:43am

Yes, i also think that sequences are absolutely important and that without sequences it doesn’t make sense to rely on metadata dictionary for DICOM attributes at all. Currently it is better to take pydicom (or low level GDCM / DCMTK for C++), if there is a requirement to access attributes.

P.S. Also, not sure it will be a good idea to add support for whole data set in meta data dictionary, but it is another, longer story.

jonasteuwen · April 14, 2020, 1:49pm

It would at least be an idea to allow the reading of the whole dictionary (just as it allows reading of the private tags), or expose a method to lookup the tag, or disable it so we can implement more efficient means using DCMTK.

jdhenckel · May 13, 2022, 4:00pm

I am using python with nibabel and pydicom and sitk cobbled together is a very awkward way. I would love to stop using the former two and use sitk exclusively… except for this ONE bug. Sequences are not supported. Can someone please fix this bug? It was reported over two years ago!

dutking · October 31, 2023, 7:41am

Issue still exists. I have just faced it trying to read Segmentation Storage dcm.