OpenDose3D YouTube channel

Alex_Vergara · January 17, 2025, 8:35pm

Hello

I want to announce the start of OpenDose3D YouTube channel.

OpenDose3D is a 3DSlicer extension for Patient dosimetry in internal radiotherapy. Please subscribe and leave us your comments.

imbeatriz · January 22, 2025, 1:39pm

Hi!

I was following the video tutorial 02 Testing OD3D and am facing a weird issue when I select the Utilities → Run Test. I receive the following message on the Python console:

[Python] DICOM test data dir: /home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Resources/DICOM/A_Cycle3-6848MBq-9h57
[Python] Successfully loaded patient 1 with StudyInstanceUID: 1.2.752.37.5.626934496.20171125.26473.4.1934 and SeriesInstanceUID: 1.3.6.1.4.1.33868.20191002120418.51247
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 48HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 4HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 1HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 24HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 1HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 96HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 24HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 48HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 4HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 96HR
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 48HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 4HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 1HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 24HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 96HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
Traceback (most recent call last):
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/OpenDose3D.py”, line 1228, in onRunTestButton
self.test.FullTest_positive()
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Logic/OpenDose3DTest.py”, line 542, in FullTest_positive
self.logic.createTransforms(referenceNode.data)
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Logic/OpenDose3DLogic.py”, line 919, in createTransforms
Elastix.RegistrationPresets_ParameterFilenames
AttributeError: module ‘Elastix’ has no attribute ‘RegistrationPresets_ParameterFilenames’
[Python] Cannot load preset. Loading failed with error: [Errno 2] No such file or directory: ‘/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/par0013Powell_NGC_singleImage.txt’
[Qt] An OpenGL Core Profile was requested, but it is not supported on the current platform. Falling back to a non-Core profile. Note that this might cause rendering issues.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://wiki.slicer.org/slicerWiki/images/2/2a/CarreraSliceEffect.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/b/b7/CurveMakerIcon.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/a/ac/ErodeDilateLabelIcon.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/a/a7/GyroGuide.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/e/e5/QuickToolsLogo.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://wiki.slicer.org/slicerWiki/images/f/f6/IntensitySegmenterIcon.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/a/ac/PAAlogo-small.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.slicer.org/slicerWiki/images/b/ba/SegAidedRegSquareFocus128.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://www.example.com/Slicer/Extensions/SlicerSurfaceLearner.png’. This content should also be served over HTTPS.
[Qt] Mixed Content: The page at ‘@KitwareMedical/slicer-extensions-webapp’ was loaded over HTTPS, but requested an insecure image ‘http://slicer.org/slicerWiki/images/3/32/T1_Mapping_Logo_Resized.png’. This content should also be served over HTTPS.
[Qt] A cookie associated with a cross-site resource at http://www.nitrc.org/ was set without the SameSite attribute. A future release of Chrome will only deliver cookies with cross-site requests if they are set with SameSite=None and Secure. You can review cookies in developer tools under Application>Storage>Cookies and see more details at Chrome Platform Status and Chrome Platform Status.

Could you help me with what could be causing this?

Thank you!

Greetings,
Beatriz

muratmaga · January 22, 2025, 4:25pm

Is the Elastix extension installed? There is an error about not finding the directory:

AttributeError: module ‘Elastix’ has no attribute ‘RegistrationPresets_ParameterFilenames’
[Python] Cannot load preset. Loading failed with error: [Errno 2] No such file or directory: ‘/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/

imbeatriz · January 22, 2025, 4:28pm

Hi,

I checked and it is installed. The name of the module tho that appears to me is SlicerElastix.

muratmaga · January 22, 2025, 4:45pm

It is not finding the registration presets. That looks like an issue with Elastix to me. Perhaps try running the Elastix by itself to register a dataset and see if it is correctly installed?

imbeatriz · January 22, 2025, 4:55pm

Hi,

I tried running Elastix by itself and it shows me this message on the python console:

[Python] Cannot load preset. Loading failed with error: [Errno 2] No such file or directory: ‘/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/par0013Powell_NGC_singleImage.txt’

I am confused because the file exists and it’s present in that directory.

muratmaga · January 22, 2025, 4:57pm

At least you know the issue with Elastix. I am not familiar with unfortunately.
So in the shell window if you do

ls -l /home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/par0013Powell_NGC_singleImage.txt

you see a file?

imbeatriz · January 22, 2025, 5:09pm

Yes I see. I even went to the directory itself and opened it.

administrator@Pacheca-IBEB:~$ ls -l /home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/Par0013Powell_NGC_singleImage.txt
-rw-r–r-- 1 administrator administrator 1796 Jan 22 16:39 /home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/SlicerElastix/lib/Slicer-5.6/qt-scripted-modules/Resources/RegistrationParameters/Par0013Powell_NGC_singleImage.txt

I think I see what is wrong. My file is called Par0013Powell_NGC_singleImage.txt while the one 3d Slicer is trying to find is par0013Powell_NGC_singleImage.txt. it’s all because of the letter P.
I just changed to a small letter p the name of the file and I don’t get the error for Elastix.

imbeatriz · January 22, 2025, 5:19pm

I still get this extensive error when I try to do the run test of OpenDose3D tho.

[Python] DICOM test data dir: /home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Resources/DICOM/A_Cycle3-6848MBq-9h57
[Python] Successfully loaded patient 1 with StudyInstanceUID: 1.2.752.37.5.626934496.20171125.26473.4.1934 and SeriesInstanceUID: 1.3.6.1.4.1.33868.20191002120418.51247
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 48HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 4HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 1HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 24HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 1HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 96HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 24HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 48HR
[Python] Cannot get DICOM slice positions for volume 1: CT SPECT-CT 4HR
[Python] Cannot get DICOM slice positions for volume 1: ACSC SPECT-CT 96HR
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 48HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 4HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 1HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 24HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] Failed to read DICOM attribute ‘DICOM.AcquisitionFramesDuration’
[Python] Attribute ‘DICOM.Acquisition.Duration’ is empty
[Python] No injection time and no timestamp in name for node 1: ACSC SPECT-CT 96HR
[Python] Failed to retrieve DICOM attribute: DICOM.Injection.Date
Traceback (most recent call last):
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/OpenDose3D.py”, line 1228, in onRunTestButton
self.test.FullTest_positive()
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Logic/OpenDose3DTest.py”, line 542, in FullTest_positive
self.logic.createTransforms(referenceNode.data)
File “/home/administrator/Software/Slicer-5.6.2-linux-amd64/slicer.org/Extensions-32448/OpenDose3D/lib/Slicer-5.6/qt-scripted-modules/Logic/OpenDose3DLogic.py”, line 919, in createTransforms
Elastix.RegistrationPresets_ParameterFilenames
AttributeError: module ‘Elastix’ has no attribute ‘RegistrationPresets_ParameterFilenames’

fragosoj · January 31, 2025, 2:29pm

This has already been fixed in the latest update of OpenDose3D (2025-01-24).

akmal871026 · February 9, 2025, 7:52am

Dear @imbeatriz ,

For version 5.8.0, its more better for OpenDose3D. Perhaps you try it. Especially in OAR segmentation, very nice.

imbeatriz · February 9, 2025, 1:13pm

Hi,

I tried and it’s working perfectly!

Thank you!

Topic		Replies	Views
OpenDose3D: A Slicer module to perform 3D patient specific dosimetry based on images in molecular radiotherapy Announcements opendose3d	3	1883	January 8, 2022
Release: OpenDose4D, (need help to finish integration) Development extensions-manager	10	594	March 19, 2020
OpenDose3D: DICOMError - Attribute 'acquisition' is empty (Siemens SPECT-CT) Support opendose3d	4	44	February 10, 2025
Pop up said that the acquisition duration Support opendose3d	0	22	June 12, 2024
OpenDose3D module is not loaded Support dicom , extensions , opendose3d	5	174	February 1, 2025

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