[ITK] [ITK-users] Problem with reading dicom series using SimpleITK

[Sara Gh]

Dear Francois,

Thank you for your helpful email.
As you said, the issue was about the series ID. I fixed the issue by making
metadata (including SeriesInstanceUID) the same for all dicom files in my
MATLAB code:

sizeP = [128 128 128]

[p,ellipse]=phantom3dAniso(sizeP);

outDir = './SLPData/';

fname = [outDir 'SLP000001.dcm'];

dicomwrite(p(:,:,i), fname);

metadata = dicominfo(fname);

for i=2:sizeP(3)

    fname = [outDir sprintf('SLP%06d.dcm', i)];

    dicomwrite(p(:,:,i), fname, metadata, 'CreateMode', 'copy');
end

Thanks,
Sara


On Thu, Nov 3, 2016 at 10:26 PM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Sara,
>
> Your code using SimpleITK is correct. I downloaded dicom images from here
> [1] and ran your code with this data and it found all the input dicom that
> were in the specified folder. Can you make sure that your output DICOM
> images from matlab are 2D images with the same series ID? My guess isthat
> your DICOMs have different seriesID, and reader.GetGDCMSeriesFileNames(pathDicomA)
> only takes the first series it finds (if no seriesID is specified).
>
> Hope this helps,
> Francois
>
>
> [1] https://midas3.kitware.com/midas/folder/7741
>
> On Thu, Nov 3, 2016 at 8:46 PM, Sara Gh <sg.ele.eng at gmail.com> wrote:
>
>> Hello,
>>
>> I have used this MATLAB
>> <https://www.mathworks.com/matlabcentral/fileexchange/50974-3d-shepp-logan-phantom> code
>> to create a stack of images using Shepp-Logan Phantom and saved all these
>> images in dicom format using *dicomwrite* function:
>>
>> sizeP = [128 128 128]
>>
>> [p,ellipse]=phantom3dAniso(sizeP);
>>
>> outDir = './SLPData/';
>>
>> for i=1:sizeP(3)
>>
>>     fname = [outDir sprintf('SLP%06d.dcm', i)];
>>
>>     dicomwrite(p(:,:,i), fname)
>> end
>>
>> So, I have 128 dicom files ('SLP000001.dcm', 'SLP000002.dcm', ... ,
>> 'SLP000128.dcm' ) in the 'SLPData' folder. Now, I am trying to read
>> these dicom images in Python using SimpleITK:
>>
>> pathDicomA = '/SLPData'
>> reader = sitk.ImageSeriesReader()
>> dicom_namesA = reader.GetGDCMSeriesFileNames(pathDicomA)
>> reader.SetFileNames(dicom_namesA)
>> imageA = reader.Execute()
>>
>> However, when I run the code, it only reads in one of the images
>> instead of the whole series:
>>
>> dicom_namesA => ('.../SLPData/SLP000108.dcm',)
>> imageA.GetSize()  => (128, 128, 1)
>>
>> I am wondering what is causing this issue and how I should resolve it?
>>
>> Thanks in advance!
>>
>> Best regards,
>> Sara
>>
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