Won't generate skeleton

[jjr30]

The software in interactive mode will open the images and runs through everything except the skeleton just fine. Once it gets to the part to generate the skeleton it runs seemingly forever without generating a model or any files about the branches. Even the test images wouldn't run either in interactive mode or in the automated mode using the provided parameter file. Screen caps of the problems are attached here.

[eobo226]

Hi, I'm experiencing the same issue. If you were able to solve it, let me know.

[gjohn1992]

Hello, was anyone able to figure this out?

[ferchaure]

I was able to make it work, updating the mex codes from the updated versions of each repository. It's tricky to do because all the code is merged together. We made a branch of the project with a few extra updates here: https://github.com/CGK-Laboratory/CellSelect-3DMorph

[NinaUME]

Hello, I am trying to use the 3DMorph Skript on a MAC but unfortunately it also does not produce any skeletons (and subsequently no branching points, nor endpoints) I could figure out that the problem is with the rk4.c file (which you find here: /3DMorph-master/Functions/FastMarching_version3b/shortestpath) which is not compiled for mac. It is no problem to recompile the other files using the "compile_c_files.m" script but the rk4.c file produces an error that shows that the function "interpgrad3d" is not properly defined. That leads to failure of generating a skeleton.
The error during the compiling looks like that:
Error using mex
Undefined symbols for architecture x86_64:
"_interpgrad3d", referenced from:
_RK4STEP_3D in rk4.o
_RK4STEP_3D in rk4.o
_RK4STEP_3D in rk4.o
_RK4STEP_3D in rk4.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Do you by chance have a rk4.mexmaci64 file that you can share or can help me with this issue?

Thank you