Batch dental segmentator: No valid volume file found in the folder

Hello!
I’m having problems with the “AutomatedDentalTools” extension.
AutomatedDentalTools contains the “BatchDentalSegmentator” module.
When I select a date folder, an error appears (No valid volume file found in the folder) when I click apply.

What could be causing this problem?
Please tell me which file extensions this module can work with?
Maybe I should change the file extension to something else?
It seems very strange to me that the module, for some reason, can’t read regular .dcm files.

I think I should clarify. There’s a neural network called NNUnet. This neural network powers the DentalSegmentator. In Slicer3D, DentalSegmentator is available in two extensions: “DentalSegmentator” itself and DentalSegmentator as part of “AutomatedDentalTools”.

When working with another extension “DentalSegmentator” such problems do not arise. In this extension, data is loaded via “add DICOM data.” I can process the same DICOM files without any problems in this extension. This gives me reason to believe my DICOM files are fine. I have worked with them for a long time without any problems.

I wanted to test whether the same “dentalsegmentator,” but as part of “BatchDentalSeg” from the “AutomatedDentalTools” extension, could perform individual segmentation of each tooth. Here, you need to specify a folder to load the data, but the program apparently doesn’t see DICOM files in the folder.

Maybe try putting your DICOM files in a folder path that does not contain special characters such as those “russian” letters between OneDrive and endodontics


I already thought about this and tried changing the file locations. Now there are no Cyrillic characters, but the error still appears.

Maybe you need to convert all your dicom studies to usual (volume) 3D image formats such as .nrrd, .nii or .nii.gz and not .dcm files

Yes, it finally worked! Thank you very much! I ran the neural network calculation and I still have to wait for it to give me the results. I hope everything works out.

Thanks for telling me to try nii.gz - at least I was able to run the neural network. It looks like it really doesn’t accept the .dcm format.