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

POSTED BY: Martijn Froeling
4 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

Hi Martijn,

I'm sorry to hear that you are having a hard time working with DICOM files in the Wolfram Language. As you correctly noticed, Import["f.dcm", "Image"] applies a number of transformations under the hood. 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 admit that our documentation for DICOM could be improved to be more helpful for advanced users. The element you are looking for is called "RawPixelData" and for now remains undocumented.

In[41]:= rawData = Import["ExampleData/head.dcm.gz", "RawPixelData"]
Out[41]= NumericArray[Type: UnsignedInteger16 Dimensions: {512, 512}]

In[42]:= MinMax[Normal @ rawData]
Out[42]= {0, 1727}

It returns an array of 16-bit unsigned integers even when the actual bit depth of the values in the file is 12, but the values are not modified in any way.

When you Import the "Data" element, on the other hand, you get the fully processed data which corresponds to the pixel values of the "Image" element:

enter image description here

Now, with "DataTransformation" -> None you can import pixel data without any scaling or other transformations defined in the DICOM file, but it will still map the theoretical range of pixel values to the range of the NumericArray type. For instance, a 12-bit DICOM data will be returned in a NumericArray of type "UnsignedInteger16" (because we don't have a 12-bit wide in the system) and every value will be multiplied by 16 (which maps [0, 2^12) to [0, 2^16)):

In[78]:= dataNoTransform = Import["ExampleData/head.dcm.gz", "Data", "DataTransformation" -> None]
Out[78]= NumericArray[Type: UnsignedInteger16 Dimensions: {512, 512}]

In[79]:= MinMax[Normal @ dataNoTransform]
Out[79]= {0, 27632}

In[80]:= MinMax[Normal @ rawData]
Out[80]= {0, 1727}

In[81]:= Max[dataNoTransform] / Max[rawData]
Out[81]= 16

One last tip: every standard DICOM tag can be imported via the "MetaInformation" element, including pixel data:

In[85]:= pixData = First @ Import["ExampleData/head.dcm.gz", {"MetaInformation", "PixelData"}]
Out[85]= NumericArray[Type: UnsignedInteger16 Dimensions: {512, 512}]

In[86]:= pixData === rawData
Out[86]= True
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
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