I’m trying to propagate the manual annotations I have, using the “Fill between slices” method.
In some volume-segmentation pairs, I get the error “Auto-complete operation skipped: all visible segments are empty”. My pipeline is always the same: load volume and segmentation → set segmentation and master volume → set visibility for all segments → initialize “Fill between slices”.
I have no clear indicator why in some volumes this works, while in others I have this problem. Do you know why this problem might occur? or point me in the direction where to search?
If I can resolve this problem I’d like to automate this process for all the volumes I have. Do you know of any snippets that might be of help?
Thank you all, have a great day!
You can only initialize “Fill between slices” if you have some non-empty visible segments. Please try with the latest Slicer Preview Release. If the problem persists then the best would be if you could share a scene (upload somewhere and post the link) where initialization fails and there are non-empty segments. Make sure no patient health information is included in publicly shared files.
thank you for your answer. Here WeTransfer - Send Large Files & Share Photos Online - Up to 2GB Free you can find one of the volume-segmentation pair that raises the error.
I had no luck in installing the Preview release since it raised the error: libITKniftiio-5.3.so.1: cannot open shared object file: No such file or directory. I don’t know if this is a common problem, I’ll try to solve it later.
As for automating the “Fill” process, can you point me in the direction of the correct API to use?
The ITK packaging issue will be fixed on Friday. Until then you can use a Slicer Preview Release from 10 days ago: https://download.slicer.org/?offset=-10.
I’ve just tested this on Linux using Slicer-4.13.0-2022-02-14 and it worked well:
I’ll try on the version you mentioned, in the meantime, I’ve managed to do it programmatically, probably I’m messing something up when using the GUI.
Thanks for the awesome support!