[ITK] Problem with Writing Dicom Series

[Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]]

For the latest stable version of SimpleITK the easiest thing to do is to set the following in the meta.yaml file:
git_tag: master
version: “master”

    regards
         Ziv

From: Sara Gh <sg.ele.eng at gmail.com>
Date: Friday, June 23, 2017 at 2:18 PM
To: "Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]" <zivrafael.yaniv at nih.gov>
Cc: "community at itk.org" <community at itk.org>
Subject: Re: [ITK] Problem with Writing Dicom Series

Dear Ziv,

Thank you for your reply. Should I change the version of SimpleITK to 1.1.0<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageSeriesReader.html> or 1.0.0?

Thanks,
Sara

On Fri, Jun 23, 2017 at 11:57 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>> wrote:
Hello Sara,

As you correctly identified, the problem is with the version of SimpleITK. The addition of the meta-data dictionaries to the series reader was done after the release of version 1.0.0.

As an immediate solution, you will need to build SimpleITK yourself. For Anaconda we have a build recipe on github: https://github.com/SimpleITK/SimpleITKCondaRecipe#process

Please follow the detailed instructions there (read all of the instructions before you start the build as you will need to change the version of SimpleITK you are building, currently set to 1.0.0 and you need master).
      regards
           Ziv

From: Sara Gh <sg.ele.eng at gmail.com<mailto:sg.ele.eng at gmail.com>>
Date: Friday, June 23, 2017 at 11:47 AM
To: "Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]" <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>>
Cc: "community at itk.org<mailto:community at itk.org>" <community at itk.org<mailto:community at itk.org>>
Subject: Re: [ITK] Problem with Writing Dicom Series

Dear Ziv,

Thank you for your reply.

I tried the sample code; however, I am getting below error:
'ImageSeriesReader' object has no attribute 'MetaDataDictionaryArrayUpdateOn'. Do you know how I should fix that? I have installed SimpleITK using python binary package for the Anaconda and currently, its version is simpleitk 1.0.0-py27_0.

Sincerely,
Sara


On Wed, Jun 21, 2017 at 10:41 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>> wrote:
Hello Sara,

Please take a look at this example on readthedocs (part of the Examples found in the SimpleITK source):
http://simpleitk.readthedocs.io/en/latest/Examples/DicomSeriesReadModifyWrite/Documentation.html

Writing a valid DICOM series which contains all of the tag information you need may be tricky, depending on the information you need to encode in the meta-data dictionary (private tags etc.).

As a side note, the problem you have with the series writer is that it is writing each of the images into its own series.

      hope this helps
              Ziv

From: Sara Gh <sg.ele.eng at gmail.com<mailto:sg.ele.eng at gmail.com>>
Date: Wednesday, June 21, 2017 at 10:19 AM
To: "community at itk.org<mailto:community at itk.org>" <community at itk.org<mailto:community at itk.org>>
Subject: [ITK] Problem with Writing Dicom Series

Hello,

I have a question regarding writing Dicom series using SimpleITK in Python. I read a 3D scan, resampled it, and stored it as a Dicom series. However, when I try to read the stored data, I am unable to load the whole 3D images and it only displays one of the slices. It seems that the header is corrupted. I would be thankful if someone could help me to fix this issue.

Here is my write method:

def WriteDicomSeries(imagein,outDir):
    writer = sitk.ImageSeriesWriter()
    filenames = [ outDir+'MR_{0:04}.dcm'.format(i) for i in range(imagein.GetSize()[2])]
    writer.SetFileNames(filenames)
    writer.Execute(imagein)

Thanks,
Sara


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