Transfer 3D Slicer segmentations to Avizo

segmentation
labelmap
#1

Hi everyone,

I have been working on segmenting micro CT data for a palaeontology specimen in 3D slicer. The files have been saved as MRB containing:
.nrrd
.seg.nrrd
.vp
.acsv (annotationROI)

In total, I have 9 different bones that I’m working on. They can export into a single OBJ containing the 9 parts that I can move around separately in Cinema 4D.

Does anyone know if it is possible to continue the segmentation in Amira Avizo software?

Thank you for your time!

Deniz

(Murat Maga) #2

I think that’s more of a Avizo question then Slicer. If you know (or find out) what input format Avizo supports for segmentation, you can ask us for guidance on how to convert your existing segmentations into those.

But I am curious what does Avizo offer in terms of segmentation that is beyond the tools available in Slicer that you want to continue with it?

1 Like
#3

Yeah I think you’re right. I’ll do some more digging.

I’m not sure but my supervisor wants to know if it can be done so I’m trying to find out.

Thanks!

Deniz

(Murat Maga) #4

Good luck. Try to convince your PI/supervisor on benefits of conducting research using the an free, open-source and extensible platform, which are mainly ease of data sharing, retention and reproducibility.