[vtkusers] What ditermines whether the slice order should be reversed?

Tue Aug 29 07:58:43 EDT 2017

Hi Liu Peng,

If you apply vtkImageFlip to the image, then the matrix returned by
reader->GetPatientMatrix() will not work with the image.  I recommend that,
at the very least, you try doing the following instead:

1) use reader->SetMemoryRowOrderToFileNative(), and
2) try using vtkDICOMToRAS instead of vtkImageFlip:
 https://github.com/dgobbi/vtk-dicom/blob/master/Source/vtkDICOMToRAS.h

Also, if possible, update to the latest version of vtk-dicom.

Cheers,
 - David

On Tue, Aug 29, 2017 at 1:58 AM, Liu_tj <tjlp at netease.com> wrote:

> Hi, David,
>
> Actually in my current code I use vtkImageFlip to flip the image data to
> solve the slice display orientation issue on coronal and saggital view as
> follow:
>
>         vtkDICOMReader* reader = vtkDICOMReader::New();
>         reader->SetFileNames(vtkDICOMFilePaths);
>         reader->Update();
>         vtkImageFlip* flip = vtkImageFlip::New();
>         flip->SetInputConnection(reader->GetOutputPort());
>         flip->SetFilteredAxis(2);
>         flip->Update();
>         vtkImageData* imageData = flip->GetOutput();
>
> Thanks
> Liu Peng
>
> 在2017-08-29，"David Gobbi" <david.gobbi at gmail.com> 写道：
>
> -----原始邮件-----
> *发件人:*"David Gobbi" <david.gobbi at gmail.com>
> *发送时间:*2017年08月29日 星期二
> *收件人:*"Liu_tj" <tjlp at netease.com>
> *抄送:*"vtkusers" <vtkusers at vtk.org>
> *主题:*Re: Re: Re: What ditermines whether the slice order should be
> reversed?
>
>
> Hi Liu Peng,
>
> For vtk-dicom, that would actually be version 0.7.1 (the current version
> is 0.8.5).
>
> It is possible that you have run into this bug, which was fixed in 0.8.3:
> https://github.com/dgobbi/vtk-dicom/issues/132
> The work-around for the bug is reader->SetMemoryRowOrderToFileNative().  See
> here for more info:
> http://dgobbi.github.io/vtk-dicom/doc/api/image_orientation.html
>
> Unfortunately, calling SetMemoryRowOrderToFileNative() doesn't work very
> well with vtkImageViewer or vtkImageViewer2, since these "viewer" classes
> insist on images that are in "bottom-to-top" order (DICOM images are
> natively in top-to-bottom order).  However, if you use vtkImageActor or
> vtkImageSlice to display your images, then you can set the camera so that
> "up" is in the correct direction.
>
> The vtkDICOMReader uses ImageOrientationPatient (0020,0037) and
> ImagePositionPatient (0020,0032) to put the slices in order.  These
> attributes are more reliable and more precise than PatientPosition
> (0018,5100).
>
> Cheers,
>  - David
>
>
>
>
> On Mon, Aug 28, 2017 at 7:03 PM, Liu_tj <tjlp at netease.com> wrote:
>
>> Hi, David,
>>
>> I forgot to mention the verison. The VTK and vtk-DICOM version are both
>> 7.1
>>
>> Thanks
>> Liu Peng
>>
>> 在2017-08-28，"David Gobbi" <david.gobbi at gmail.com> 写道：
>>
>> -----原始邮件-----
>> *发件人:*"David Gobbi" <david.gobbi at gmail.com>
>> *发送时间:*2017年08月28日 星期一
>> *收件人:*"Liu_tj" <tjlp at netease.com>
>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>> *主题:*Re: Re: What ditermines whether the slice order should be reversed?
>>
>>
>> Hi Liu Peng,
>>
>> What versions of VTK and vtk-dicom you are using?
>>
>>  - David
>>
>> On Mon, Aug 28, 2017 at 12:31 AM, Liu_tj <tjlp at netease.com> wrote:
>>
>>> Hi, David,
>>>
>>> As far as I know, in the RCS system, the direction of Z axis is from
>>> foot to head.So by default, the slice order in your dicom reader is
>>> consistent with the RCS system.When the reader sorts the slices, does it
>>> consider the Patient Postion tag(0080,5100)? Some doctors might use some
>>> DICOM tools which the slice order is from head to foot and get used to that.
>>>
>>> My code block for load slices is as follow:
>>>
>>>        vtkStringArray* vtkDICOMFilePaths = vtkStringArray::New();
>>>         vtkDICOMFilePaths->SetNumberOfValues(aDICOMFilePaths->Length);
>>>         for(int i = 0; i < aDICOMFilePaths->Length; i ++)
>>>         {
>>>             String^ filePath = aDICOMFilePaths[i];
>>>             const char* filePathByChars = MDKStringUtility::NStringToCha
>>> rs(filePath);
>>>
>>>             vtkDICOMFilePaths->SetValue(i, filePathByChars);
>>>         }
>>>
>>>         vtkDICOMReader* reader = vtkDICOMReader::New();
>>>         vtkImageData* imageData = reader->GetOutput();
>>>
>>> Thanks
>>> Liu Peng
>>> 在2017-08-28，"David Gobbi" <david.gobbi at gmail.com> 写道：
>>>
>>> -----原始邮件-----
>>> *发件人:*"David Gobbi" <david.gobbi at gmail.com>
>>> *发送时间:*2017年08月28日 星期一
>>> *收件人:*"Liu_tj" <tjlp at netease.com>
>>> *抄送:*"vtkusers" <vtkusers at vtk.org>
>>> *主题:*Re: What ditermines whether the slice order should be reversed?
>>>
>>>
>>> Hi Liu Peng,
>>>
>>> The vtkDICOMReader sorts according to the Image Plane Module:
>>> http://dicom.nema.org/MEDICAL/dicom/current/output/chtml/par
>>> t03/sect_C.7.6.2.html
>>> That is, the slices are sorted in a manner such that the VTK image data
>>> has a right-handed coordinate system (called an RCS in the link above).
>>>
>>> Sorting the slices to get an RCS means that sometimes the slices will be
>>> sorted the same as the InstanceNumber, and sometimes they will be sorted
>>> opposite to InstanceNumber, depending on the order in which scanner ordered
>>> the slices.
>>>
>>> You can perform the sorting yourself by calling reader->SortingOff().
>>> If Sorting is Off, the reader will take the slices in the same order as the
>>> vtkStringArray that you passed to reader->SetFileNames().
>>>
>>> If you send me the block of code where you set up and call the reader,
>>> then I might be able to provide more help.  Don't forget to also say what
>>> versions of VTK and vtk-dicom you are using.
>>>
>>> Cheers,
>>>  - David
>>>
>>>
>>>
>>> On Sun, Aug 27, 2017 at 10:41 AM, Liu_tj <tjlp at netease.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a question about the DICOM slice order. I use the DICOM reader
>>>> by David Gobbi to read the slice series to vtkImageData. And I found that
>>>> the oder is the same as the order by DICOM instanceNumber tag. However,
>>>> some doctors tell me that the order should be reversed because the scan
>>>> should start from head to foot.
>>>>
>>>> @David, if I need to reverse, how to achieve that by your DICOM reader?
>>>>
>>>> Thanks
>>>> Liu Peng
>>>>
>>>
>
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