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Load DICOM with actual data values: Import/Export changes data

POSTED BY: Martijn Froeling
5 Replies

Importing a list of specific tags in one call to Import is not possible right now, but we will try to add support for this in the next release. Currently, MetaInformation can only handle one subelement which must be a string. In the simplest case this will be a name of a DICOM tag, e.g. "PixelData", but it is possible to pass a simple pattern to import a bunch of related tags at once, for instance:

In[94]:= Import["ExampleData/head.dcm.gz", {"MetaInformation", "PatientName"}]

Out[94]= "Male 1958 Anonymous"

In[95]:= Import["ExampleData/head.dcm.gz", {"MetaInformation", "Patient*"}]

Out[95]= <|"PatientName" -> "Male 1958 Anonymous", 
 "PatientID" -> "GH-WISE:68736", "PatientSex" -> "M", 
 "PatientBirthName" -> "anonymous", 
 "PatientMotherBirthName" -> "anonymous", 
 "PatientTelephoneNumbers" -> "anonymous", 
 "PatientReligiousPreference" -> "anonymous", 
 "PatientComments" -> "anonymous", "PatientPosition" -> "HFS"|>

That being said, you can still read a list of tags without calling Import multiple times if you are willing to use DICOMTools paclet directly (Import uses this paclet under the hood). Paclet functions are not documented and we don't guarantee backwards compatibility for them, but they often offer more flexibility then Import interface:

 In[97]:= Needs["DICOMTools`"]

 In[98]:= file = First @ ExtractArchive @ FindFile @ "ExampleData/head.dcm.gz";

 In[99]:= DICOMTools`ReadMetadata[file, {"PatientName", "RescaleSlope", "RescaleIntercept"}]

 Out[99]= <|"PatientName" -> "Anonymous^Male 1958",  "RescaleSlope" -> "1.53968253968253", "RescaleIntercept" -> "0.0"|>

Two things to notice: paclet only works with full paths and does not handle compressed DICOMs, so we need an extra step to uncompress the sample file and secondly, values are imported as they are stored in the file, without post-processing or formatting (so for instance, numbers are imported as strings and dates will not be automatically converted to WolframLanguage DateObjects).

If you wish to format the returned data, another step is needed:

In[113]:= rawMeta = DICOMTools`ReadMetadata[file, {"PatientName", "RescaleSlope", "RescaleIntercept"}]

Out[113]= <|"PatientName" -> "Anonymous^Male 1958",  "RescaleSlope" -> "1.53968253968253", "RescaleIntercept" -> "0.0"|>

In[114]:= DICOMTools`ConvertMetadata[file][rawMeta]

Out[114]= <|"PatientName" -> "Male 1958 Anonymous", "RescaleSlope" -> 1.5396825, "RescaleIntercept" -> 0.|>

To answer your second question - Import only supports tag keywords, but the paclet can read tags using (group, elem) values. They can be specified in the form: {"GGGG", "EEEE"} (leading 0s can be omitted). For example:

In[105]:= DICOMTools`ReadMetadata[file, {{"0028", "1053"}, {"10", "40"}}]

Out[105]= <|"RescaleSlope" -> "1.53968253968253", "PatientSex" -> "M"|>

In the returned Association tag names are used as keys anyway, but if you prefer, you can always replace any tag name with its group-elem id using the following function:

In[107]:= DICOMTools`GetGroupElemNumbers["PixelData"]

Out[107]= {"7FE0", "10"}

In[108]:= DICOMTools`GetGroupElemNumbers["PatientAge"]

Out[108]= {"10", "1010"}

There is also a reverse function:

In[109]:= DICOMTools`GetKeyword[{"7FE0", "0010"}]

Out[109]= "PixelData"

In[110]:= DICOMTools`GetKeyword[{"10", "1010"}]

Out[110]= "PatientAge"

Notice that it only works with standard DICOM tags. I guess that 2005_100e that you use in your example is vendor-specific and so the paclet will not know its name:

In[111]:= DICOMTools`GetKeyword[{"2005", "100e"}]

Out[111]= "Unknown Tag & Data"
POSTED BY: Rafal Chojna

Awesome! Very helpful information!

I was not aware of the DICOMTools will dig a bit into that.

And indeed the 2005 tag is a vendor-specific one, if i remember correctly all odd first numbers are generally vendor-specific.

Thanks again for the information!

POSTED BY: Martijn Froeling
POSTED BY: Rafal Chojna

Awesome, that was exactly what I was looking for!!!

Thanks for the explanations, always nice to learn a few new things, I was not aware that with {"MetaInformation", "xxx"} you can only import specific tags.

Two additional questions if i may:

  1. Is loading multiple tags in one go possible based on the help of Import this should work right? enter image description here

These examples do not work or am I again missing something.

    Import["data\\dcm\\001_v1\\01901_T1_enhanced_(3x8mm)\\00001.dcm", \
    {"MetaInformation", "2005_100e", "RescaleSlope", "RescaleIntercept"}]
    Import["data\\dcm\\001_v1\\01901_T1_enhanced_(3x8mm)\\00001.dcm", \
    {"dicom", "MetaInformation", "2005_100e", "RescaleSlope", 
      "RescaleIntercept"}]
  1. For known Dicom tags only the Name is exposed, but not the orriginal tag, is this correct? For exmaple Pixel Data has tag (7FE0,0010)

    (*works*)
    Import["data\\dcm\\001_v1\\01901_T1_enhanced_(3x8mm)\\00001.dcm", \
    {"MetaInformation", "PixelData"}]
    (*does not work*)
    Import["data\\dcm\\001_v1\\01901_T1_enhanced_(3x8mm)\\00001.dcm", \
    {"MetaInformation", "7FE0_0010"}]
    

Thanks again for the support!

Best Martijn

PS Dicom support came a long way, I remember using MathVisionTools for Dicom support back in my university days

POSTED BY: Martijn Froeling

I am coming upon this interesting thread years later. I want to comment on the sentence, "We went for this design because otherwise a vast majority of DICOM files would return an all-black image by default, which wouldn't be very useful." I think there's a hidden assumption about to whom the functionality is meant to be useful.

With automatic transformation and glossy images, Import[]'s DICOM handling is useful to non-professionals who want to quickly put an existing DICOM image in a format that is easy to qualitatively analyze. That may be useful to patients who are generating informed questions for their healthcare providers. It is also useful to people who are running demos of Wolfram's functionality to generate sales.

With automatic transformation and glossy images, Import[]'s DICOM handling is NOT useful to healthcare providers, because as the OP mentioned: "...based on what I see actual values of the data are changed by clipping the histogram, which for default handling of medical data is never OK!!" Conventions like this are very serious in medicine because doctors need images free of manipulations that could affect the interpretation of key features of the image. So anyone who wanted to build a medical image processing app in Mathematica that meets government standards would have to show they are explicitly working around this default behavior.

Without automatic transformation, Importing a DICOM indeed gets you mostly-black images initially, but it seems that is what's useful to researchers. The OP was a very polite way of saying that without the ability to extract the raw voxel values, Wolfram's exciting new Import functionality for DICOMs was effectively useless to researchers. And the solution was for researchers to use a then-undocumented "RawPixelData" tag. (There's a single line about it in this article https://reference.wolfram.com/language/ref/format/DICOM.html now... was that there 4 years ago?) But in research, reproducibility is paramount, and reproducibility is curtailed greatly by "black box" functionality in software.

I wonder if sometimes the community would be better served by more candor and clarity about which functionality is meant to be useful to which users. Right now the main documentation page for DICOM reads like it's geared toward people who have never heard of a DICOM image until that day, and it's very important to keep that language in place in order to continue facilitating learning. But the info a researcher needs to do even 1 micro-step of their work ("RawPixelData" --> "DICOM pixel data without scaling") is buried in the Import Elements section, and a person who doesn't read that far is making a rational choice since Wolfram documentation just doesn't always cover the relevant technical information. This post was a demonstration of someone having to figure out for themself what's happening "under the hood" in order to make the functionality useful for their application area.

A fix could possibly look like creating an "Application Areas" section on documentation pages. For the DICOM page (https://reference.wolfram.com/language/ref/format/DICOM.html) that section would be close to the top and it would say something right at the beginning like:

"Import[] by default scales pixel values by clipping the histogram to ensure that the first image generated from the data has visible features. Researchers who want to perform a quantitative analysis must Import the "RawPixelData" element or Import with "DataTransformation" -> None".

Doing this would potentially allow researchers to get to their real work faster, without compromising other people's learning.

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