[vtkusers] Problem using vtkDicomWriter

[David Gobbi]

Hi Eddy,

The SOPInstanceUID must be different for each image (and the other two UIDs
shouldn't be the same as the SeriesInstanceUID, either).

What version of vtk-dicom are you using, and what operating system?  I can
check on my end to make sure that the random numbers for the UUIDs are
being properly generated.  I use CryptGenRandom() on Windows and
/dev/urandom on UNIX/Linux.

 - David

On Thu, Jan 26, 2017 at 9:05 AM, Eddy Cappeau <edcpwk at gmail.com> wrote:

> Hi David,
>
> When I load the DICOM directory, Slicer tells me that there's only one
> serie.
> Each image have the same SeriesInstanceUID.
>
> I don't know if it's normal but the SeriesInstanceUID is also used for the
> SOPInstanceUID, the StudyInstanceUID and the FrameOfReferenceUID.
>
> I've made a screenshot of the Slicer metadata browser here :
>
> https://framapic.org/t3tTt1RHhlWP/XhHP9dQ2Nz8s.png
>
>
> Eddy
>
>
> 2017-01-26 15:43 GMT+01:00 David Gobbi <david.gobbi at gmail.com>:
>
>> Hi Eddy,
>>
>> In Slicer's DICOM browser, does it show all of the images as belonging to
>> the same series?  I'm wondering if, perhaps, each image has a different
>> SeriesInstanceUID.  That would definitely cause problems with loading into
>> a "dicom aware" program like Slicer, but ParaView probably wouldn't care.
>>
>>  - David
>>
>> On Thu, Jan 26, 2017 at 7:30 AM, Eddy Cappeau <edcpwk at gmail.com> wrote:
>>
>>> Hi Andras,
>>>
>>> I didn't manage to load un single image before.
>>>
>>> Thank you for the tip.
>>>
>>> Eddy
>>>
>>> 2017-01-26 15:28 GMT+01:00 Eddy Cappeau <edcpwk at gmail.com>:
>>>
>>>> Hello David,
>>>>
>>>> I used the vtkDICOMMRGenerator filter, unsigned short instead of
>>>> unsigned char and add this line :
>>>>
>>>>      meta->SetAttributeValue(DC::SpacingBetweenSlices, "1");
>>>>
>>>> The BitsAllocated has now a value of 16 but I've got the same result.
>>>>
>>>> Thanks to the tips given by Andras, I've opened each slice individually
>>>> and they seems correct.
>>>>
>>>> There's definitly something wrong in my files, but I don't see why.
>>>>
>>>> Thanks.
>>>>
>>>> Eddy
>>>>
>>>> 2017-01-25 14:35 GMT+01:00 David Gobbi <david.gobbi at gmail.com>:
>>>>
>>>>> Hi Eddy,
>>>>>
>>>>> The code is using a vtkDICOMCTGenerator to write an MR image, which is
>>>>> definitely wrong.  Use the vtkDICOMMRGenerator, and make sure the meta data
>>>>> matches the IOD: http://dicom.nema.org/med
>>>>> ical/dicom/current/output/chtml/part03/sect_C.8.3.html
>>>>>
>>>>> The standard says that BitsAllocated must be 16 for MR images,
>>>>> therefore an 8-bit MR image is non-standard and DICOM software may to
>>>>> refuse to display it.  You should convert your data to 16-bit (In fact, it
>>>>> seems fishy that you are working with unsigned char, since if you are
>>>>> writing a reformat of an MR image, then wasn't the original MR image a
>>>>> 16-bit image?)
>>>>>
>>>>> I can't answer about why Slicer is only showing one slice, as I don't
>>>>> currently have Slicer installed.
>>>>>
>>>>>  - David
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Jan 25, 2017 at 1:57 AM, Eddy Cappeau <edcpwk at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Here's the code below. This is almost the example of the api doc :
>>>>>>
>>>>>>     auto generator = vtkSmartPointer <vtkDICOMCTGenerator>::New();
>>>>>>     vtkSmartPointer <vtkDICOMMetaData> meta = vtkSmartPointer
>>>>>> <vtkDICOMMetaData>::New();
>>>>>>
>>>>>>     meta->SetAttributeValue(DC::PatientName, "Test");
>>>>>>     meta->SetAttributeValue(DC::PatientID, "0000001");
>>>>>>     meta->SetAttributeValue(DC::ScanOptions, "");
>>>>>>     meta->SetAttributeValue(DC::ScanningSequence, "GR");
>>>>>>     meta->SetAttributeValue(DC::SequenceVariant, "SP");
>>>>>>     meta->SetAttributeValue(DC::ScanOptions, "");
>>>>>>     meta->SetAttributeValue(DC::MRAcquisitionType, "2D");
>>>>>>
>>>>>>     vtkSmartPointer <vtkDICOMWriter> dicom_writer =
>>>>>>         vtkSmartPointer <vtkDICOMWriter>::New();
>>>>>>     dicom_writer->SetInputData(img);
>>>>>>     dicom_writer->SetMetaData(meta);
>>>>>>     dicom_writer->SetGenerator(generator);
>>>>>>     dicom_writer->SetSeriesDescription("Sagittal Multi-planar
>>>>>> Reformat");
>>>>>>
>>>>>>     // Set the output filename format as a printf-style string.
>>>>>>     dicom_writer->SetFilePattern("%s/IM-0001-%04.4d.dcm");
>>>>>>     // Set the directory to write the files into.
>>>>>>     dicom_writer->SetFilePrefix(path.toStdString().c_str());
>>>>>>     // Write the file.
>>>>>>     dicom_writer->Write();
>>>>>>
>>>>>> Sorry, the use of an unsigned short type was a carreless mistake. The
>>>>>> result is better with unsigned char,
>>>>>> but I still see just one image of the serie on 3D Slicer. Is there
>>>>>> something missing to have a complete serie ?
>>>>>>
>>>>>> I didn't know the vtkImageImport and I'll give it a try.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Eddy
>>>>>>
>>>>>>
>>>>>> 2017-01-24 15:41 GMT+01:00 David Gobbi <david.gobbi at gmail.com>:
>>>>>>
>>>>>>> Hi Eddy,
>>>>>>>
>>>>>>> Can you provide the code that you used to write the image with
>>>>>>> vtkDICOMWriter?  Here is an example:
>>>>>>> http://dgobbi.github.io/vtk-dicom/doc/api/image_writer.html
>>>>>>>
>>>>>>> Creating an image with a loop that calls GetScalarPointer() for
>>>>>>> every pixel is not very efficient, and casting to a "char *" when the data
>>>>>>> is "unsigned short" is wrong: you are setting only 8 bits of each 16-bit
>>>>>>> pixel, while leaving the other 8 bits uninitialized.  The vtkImageImport
>>>>>>> filter is a better way of generating image data:
>>>>>>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Images/ImageImport
>>>>>>>
>>>>>>>  - David
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jan 24, 2017 at 2:51 AM, Eddy Cappeau <edcpwk at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I'd like to use the vtkDICOMWriter class to convert a vtkImage to a
>>>>>>>> set of DICOM images.
>>>>>>>>
>>>>>>>> I've compile VTK with the vtkDICOM module enabled and followed the
>>>>>>>> example from the pdf found on the github repository (
>>>>>>>> http://dgobbi.github.io/vtk-dicom/doc/vtk-dicom.pdf).
>>>>>>>>
>>>>>>>>
>>>>>>>> The image data is created like this :
>>>>>>>>
>>>>>>>>     auto  img = vtkSmartPointer < vtkImageData >::New();
>>>>>>>>     img->SetOrigin(0, 0, 0);
>>>>>>>>     img->SetDimensions(1024, 1024, numlayer);
>>>>>>>>     img->SetSpacing(1, 1, 1);
>>>>>>>>     img->AllocateScalars(VTK_UNSIGNED_SHORT, 1);
>>>>>>>>
>>>>>>>> and the data filled like this :
>>>>>>>>
>>>>>>>>            for (int n = 0; x < numlayer; n++) {
>>>>>>>>                 for (int x = 0; x < 1024; x++) {
>>>>>>>>                     for (int y = 0; y < 1024; y++) {
>>>>>>>>                         char* pixel = static_cast<char*>(img->GetScalarPointer(x,
>>>>>>>> y, n));
>>>>>>>>                         pixel[0] = values[x][y];
>>>>>>>>                     }
>>>>>>>>
>>>>>>>> I can load the converted result with paraview without problems.
>>>>>>>> But with 3D Slicer, I can just load the first file of the serie and
>>>>>>>> it display a blank image.
>>>>>>>>
>>>>>>>> What do I have to do to be able to load the images with both
>>>>>>>> application ?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Eddy
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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