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

[David Gobbi]

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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