[vtkusers] Problem using vtkDicomWriter

[Eddy Cappeau]

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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