MorphoSource data and dealing with DICOM series in Slicer

DICOM is a standard image data format that is designed to facilitate data exchange between medical imaging facilities. While it is a standard, manufacturers of imaging equipment implemented the format in different ways, which can be a amajor headache. Slicer has a robust DICOM import/export module. It should read almost all well-structured DICOM series. For the ones that fail, DICOM patcher can be used to strip the meta data portion of DICOM and just load the image.

For this tutorial, I will use a DICOM series from the excellent MorphoSource repository (http://morphosource.org/Detail/MediaDetail/Show/media_id/4963). You may have to register for the site to download the data. Registration is well worth the hassle, as it provides thousands of scanned vertebrate specimens in a very nicely curated manner. I also chose MorphoSource, because recently a user had issues getting the data into Slicer. The solution here is based on the response from the Andras Lasso (Thanks Andras!).

Download the zip file (1.9GB) and unzip it to a folder. Open the DICOM module, Click Import and navigate a few folders down to the Saimiri_20187 folder, and hit OK. You can either choose to incorporate the DICOM sequence into the DICOM database or simply link the files. If you choose the latter, and later change or remove the location of Saimiri_20187 folder, you won’t be able to reload your data. This is really a moot point, as in the end we will save the dataset as NRRD or NII, which are far more suitable for our purposes than image sequences.

Slicer will begin loading the DICOM series, and eventually will display a message saying 0 Patient/Studies/Series were imported. We can dig further on the root cause of the problem by hitting CTRL+0 and bringing the Log Messages dialog box. If you scroll down, you should see  error messages labeled critical. It complains about dataset missing the patient and study name, as well as an Unknown DICOM tag. So nothing is loaded.

To fix this problem, open the DICOM Patcher module, specify Saimiri_20187 folder as the DICOM Input, and choose an output folder. Make sure Generate missing patient/study/series ID is checked and hit Patch. This will recreate the DICOM series in the specified folder.

Once patching is completed, you can use the DICOM browser to import the patched dataset. Notice how slow it is now importing (as it should, this is a massive 3GB dataset). Once DICOM browser completes the import, you should now have a record called Saimiri_201870000.dcm click on it and hit load. Once it is loaded, you can cross reference the metadata (namely image dimensions and spacing) from MorphoSource to the values reported by the Volume module. They should be identical.

Remember to save your resultant dataset as Nifti or NRRD.

 

 

5 thoughts on “MorphoSource data and dealing with DICOM series in Slicer

  1. Sherman

    Thanks.
    By the way, I can only find the module of “Philips 4D US Dicom patcher” .
    Is it the patcher you mentioned?
    When I patch it. it shows “Not Philips 4D ultrasound DICOM file. Skipped.”

    Reply
    1. maga Post author

      It should come default with a recent version of the SLicer. Use the module search button and type ‘patcher’.
      M

      Reply
        1. maga Post author

          It might be related to your locale (language and font) settings on your computer. I suggest contacting the slicer support group at discourse.slicer.org

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