How to adjust the distorted image?

pieper · November 14, 2017, 6:06pm

Looking at this a bit more, it’s clear that these are pretty non-standard files.

Running @dclunie’s verifier points out that the file is internally inconsistent.

$ dciodvfy /tmp/3dslicer\ test/Ferrassie\ 1-MbsSup.0135.dcm
...
Error - Media Storage SOP Class UID different from SOP Class UID
...

The media class is the DCMTK private class while the image SOP class is Secondary Capture. Because of this GDCM looks for spacing in tag 0x0018,0x2010 while the file actually has it in 0x0028,0x0030.

I guess the best for you @laura_rodriguez might be to look into the history of these files and see if any of the DICOM information can be relied on. If not maybe save them in a less ambiguous way, either as fixed DICOM or maybe in nrrd or similar format.

For the record some of the related GDCM code is linked below.

github.com

Slicer/ITK/blob/slicer-v4.12.0-2017-05-09-2d63918/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmPixmapReader.cxx#L72-L170


bool res = false;
/* Does it really make sense to check for Media Storage SOP Class UID?
 * I need then to check consistency with 0008 0016 Instance SOP Class UID
 * ... I don't think there is an end.
 * I'd rather go the old way check a bunch of tags (From Image Plane
 * Module).
 */
MediaStorage ms = header.GetMediaStorage();
bool isImage = MediaStorage::IsImage( ms );
if( isImage )
  {
  // I cannot leave this here, since ELSCINT1 / LOSSLESS RICE declares CT Image Storage,
  // when in fact this is a private Media Storage (no Pixel Data element)
  //assert( ds.FindDataElement( Tag(0x7fe0,0x0010 ) ) );
  assert( ts != TransferSyntax::TS_END && ms != MediaStorage::MS_END );
  // Good it's the easy case. It's declared as an Image:
  //PixelData->SetCompressionFromTransferSyntax( ts );
  res = ReadImage(ms);
  }
//else if( ms == MediaStorage::MRSpectroscopyStorage )

This file has been truncated. show original

github.com

Slicer/ITK/blob/slicer-v4.12.0-2017-05-09-2d63918/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx#L1219


    // -> (0018,1063) DS [76.000000]                              #  10, 1 FrameTime


    gdcmWarningMacro( "No spacing value found" );
    sp.push_back( 1.0 );
    sp.push_back( 1.0 );
    sp.push_back( 1.0 );
    return sp;
    }
  }


Tag spacingtag = GetSpacingTagFromMediaStorage(ms);
if( spacingtag != Tag(0xffff,0xffff) && ds.FindDataElement( spacingtag ) && !ds.GetDataElement( spacingtag ).IsEmpty() )
  {
  const DataElement& de = ds.GetDataElement( spacingtag );
  const Global &g = GlobalInstance;
  const Dicts &dicts = g.GetDicts();
  const DictEntry &entry = dicts.GetDictEntry(de.GetTag());
  const VR & vr = entry.GetVR();
  assert( vr.Compatible( de.GetVR() ) );
  switch(vr)
    {

github.com

Slicer/ITK/blob/slicer-v4.12.0-2017-05-09-2d63918/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx#L1048-L1056


case MediaStorage::SecondaryCaptureImageStorage:
case MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage:
case MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage:
case MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage:
case MediaStorage::MultiframeTrueColorSecondaryCaptureImageStorage:
  // See PS 3.3-2008. Table C.8-25 SC IMAGE MODULE ATTRIBUTES
  // and Table C.8-25b SC MULTI-FRAME IMAGE MODULE ATTRIBUTES
  t = Tag(0x0018,0x2010);
  break;

Topic		Replies	Views
Is it possible to edit the ImageOrientationPatient DICOM tag in slicer? Support registration	6	2450	June 25, 2025
Gantry tilt correction in CT DICOMS Support dicom	3	1601	August 31, 2021
Distorted & malaligned volumes after loading DICOM sets Support dicom , volume	12	821	November 13, 2023
Can't load dicom images generated by dcmtk Support dicom	26	3173	September 17, 2019
Problem with sagittal and coronal view from CCTA DICOM files Support dicom	15	3245	August 3, 2017

How to adjust the distorted image?

Related topics