[slicer-users] DICOM RT export: the .rtss file is not created

M.A. Piliero mpiliero at gmail.com
Wed Mar 1 05:29:25 EST 2017


Dear Csaba,

I have just tried to export to DICOM RT with the fix you have suggested.
The .rtss file is created but the images are uniform, full of zeros.

Regards,
Maria Antonietta

2017-02-28 17:22 GMT+01:00 Csaba Pinter <csaba.pinter at queensu.ca<mailto:csaba.pinter at queensu.ca>>:
Thanks for the answer, makes a lot of sense!

OK so your workflow is correct, so it’s probably the error message from Reporting (that Greg highlighted) that prevents the RT plugin from working correctly. Could you please try the following?
1. Open C:/Users/ietta/AppData/Roaming/NA-MIC/Extensions-25516/Reporting/lib/Slicer-4.6/qt-scripted-modules/DICOMSegmentationPlugin.py
2. Go to line 306, and instead of
  instanceUIDs = node.GetAttribute("DICOM.ReferencedInstanceUIDs").split()
enter this:
  instanceUIDs = []
  if node.GetAttribute("DICOM.ReferencedInstanceUIDs") is not None:
    instanceUIDs = node.GetAttribute("DICOM.ReferencedInstanceUIDs").split()
Please pay close attention to the indentation (spaces before the lines)
4. Start Slicer and do the same you did before

If it works, then this fix could be applied to the Reporting extension for 4.6.

Thanks,
csaba

From: M.A. Piliero [mailto:mpiliero at gmail.com<mailto:mpiliero at gmail.com>]
Sent: Tuesday, February 28, 2017 10:55
To: Csaba Pinter <csaba.pinter at queensu.ca<mailto:csaba.pinter at queensu.ca>>
Cc: Sharp, Gregory C. <GCSHARP at partners.org<mailto:GCSHARP at partners.org>>; SPL Slicer Users <slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>>

Subject: Re: [slicer-users] DICOM RT export: the .rtss file is not created

Dear Gregory and Csaba,

thank you for your prompt answers.

What I would like to do is segmenting some ROIs in the PET data set and then export the images and the ROI structures as DICOM-RT.
I need to use this output as input to another software. The instructions on this software explain how to do the segmentations and export the DICOM RT files using Slicer version 3. The output should be a set of images together with the .rtss file. I am trying to obtain the same output using Slicer version 4.

I did the following steps:
1) Import the PET data set from the patient folder. The WB 3D AC volume is created.
2) Using the old Editor I draw the ROI (tissue 1). The WB 3D AC-Label volume is created.
I am not using the new editor because I cannot understand how to create the label map.
3) Then I go to Model Maker, select the WB 3D AC-Label as Input Volume, Create New ModelHierarchy in Models (the word Models appears), and tissue_model as Model Name. The tissue_model_1_tissue model is created.
4) Then I go to Segmentations, Create New segmentation. In the Copy/move tab I select the model on the right (tissue_model_1_tissue) e click on <+. The Segmentation structure with my tissue ROI is created.
5) Finally, I go to SubjectHierarchy and move the model (tissue_model_1_tissue), the LabelMap volume (WB 3D AC-Label) and the Segmentations inside the study (PET globale corporea).
6) Right Click on the study, Export to DICOM. In the select export type tab I select RT (30% 2 series), I choose the folder where I want to put the output (a different folder from the patient folder), and then click on export.

I hope such details will help to understand what I am doing wrong.

Thank you for your help,
Maria Antonietta

2017-02-28 15:18 GMT+01:00 Csaba Pinter <csaba.pinter at queensu.ca<mailto:csaba.pinter at queensu.ca>>:
Hi Maria Antonietta,

It seems to me that you want to use the Reporting extension to export DICOM SEG object. This is not in sync with the email subject which says that you want to export DICOM-RT. Can you please tell us your goal?

Also Greg’s questions are relevant, it is important to know what you used to create the segmentation.

Thanks,
csaba

From: slicer-users [mailto:slicer-users-bounces at bwh.harvard.edu<mailto:slicer-users-bounces at bwh.harvard.edu>] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, February 28, 2017 08:55
To: 'M.A. Piliero' <mpiliero at gmail.com<mailto:mpiliero at gmail.com>>
Cc: SPL Slicer Users <slicer-users at bwh.harvard.edu<mailto:slicer-users at bwh.harvard.edu>>
Subject: Re: [slicer-users] DICOM RT export: the .rtss file is not created

Hi Maria Antonietta,

Thank you for the log file.  The below is possibly the interesting part.

Traceback (most recent call last):
  File "<string>", line 5, in <module>
  File "C:/Users/ietta/AppData/Roaming/NA-MIC/Extensions-25516/Reporting/lib/Slicer-4.6/qt-scripted-modules/DICOMSegmentationPlugin.py", line 306, in examineForExport
    instanceUIDs = node.GetAttribute("DICOM.ReferencedInstanceUIDs").split()
AttributeError: 'NoneType' object has no attribute 'split'

I may need a few moments/days to review the current implementation and diagnose.

How did you originally create the segmentation?  Using the editor?  (Old editor or new editor?)

Greg

From: slicer-users [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of M.A. Piliero
Sent: Tuesday, February 28, 2017 6:16 AM
To: Sharp, Gregory C.
Cc: SPL Slicer Users
Subject: Re: [slicer-users] DICOM RT export: the .rtss file is not created

Dear Gregory,

I just noticed that the error log file was much bigger than the screenshot I posted.
I have put in attachment the full Error Log file.
I am sorry for the inconvenience.

Regards,
Maria Anotnietta

2017-02-22 17:03 GMT+01:00 M.A. Piliero <mpiliero at gmail.com<mailto:mpiliero at gmail.com>>:
Dear Gregory,

please find attached a screenshot of the error log.

Thank you,
Maria Antonietta

2017-02-22 16:34 GMT+01:00 Sharp, Gregory C. <GCSHARP at partners.org<mailto:GCSHARP at partners.org>>:
Dear Maria Antonietta,

Please keep the e-mail list in cc, it helps other users with the same problem.
The method to copy an error log is here:

https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/ErrorLog

Thank you,
Greg

From: M.A. Piliero [mailto:mpiliero at gmail.com<mailto:mpiliero at gmail.com>]
Sent: Wednesday, February 22, 2017 10:28 AM
To: Sharp, Gregory C.
Subject: Re: DICOM RT export: the .rtss file is not created

Dear Gregory,

I don't have any error. The dicom images are created fine but the rtss file is not created.

Maria Antonietta

2017-02-22 15:45 GMT+01:00 Sharp, Gregory C. <GCSHARP at partners.org<mailto:GCSHARP at partners.org>>:
Dear Maria,

Your selection in the UI looks ok to me.  Could you please send us the error log?

Greg

From: slicer-users [mailto:slicer-users-bounces at bwh.harvard.edu<mailto:slicer-users-bounces at bwh.harvard.edu>] On Behalf Of M.A. Piliero
Sent: Wednesday, February 22, 2017 7:44 AM
To: SPL Slicer Users
Subject: [slicer-users] DICOM RT export: the .rtss file is not created

Dear Slicer Community,

I am trying to export a study using the DICOM RT Export module but the .rtss file doesn't show up. I have tried following the instructions given by Csaba at http://massmail.spl.harvard.edu/public-archives/slicer-users/2015/009399.html but the .rtss file is still not created.

I cannot understand what I am doing wrong.
I have attached a screenshot of the Subject Hierarchy and the DICOM Export window.

Any help is much appreciated.
Regards,
Maria Antonietta


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