[vtkusers] Problem using vtkDicomWriter

[Eddy Cappeau]

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/medical/dicom/current/output/chtm
>> l/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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