[vtkusers] Problem using vtkDicomWriter

[Eddy Cappeau]

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/medical/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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