swc.shape and soma.save, soma.pad don't exist

[rivuletstudio]

swc.shape and soma.save, soma.pad don't exist

[donghaozhang]

soma is mainly for neuron images. to my understanding you are doing vessels why you need soma?

[hanke580]

I just want to test if this algorithm can be adopted to vessel tracing, cuz some other neuron tracing methods like snake have been adopted to this area and got decent results.
The results in your paper is very charming, so I want to have a try

[donghaozhang]

I think it can be adapted to vessel tracing, but I do not suggest you trying this option --save-soma. You can start from the following line: rtrace -f example.mhd -t 10 --tracing_resolution 1.5 --vtk

[donghaozhang]

If there is no shape of swc, it maybe be caused by your input image. Can I see maximum intensity projection of your input image?

[hanke580]

I use swc._data.shape() and it worked!
My input is CTA intracranial image in nii format, and I have also got tracing result.
Thanks a lot!
By the way, do you know how to convert swc format into 3-D array format? Since I want to mark the tracing result back to the original image and see if the results are good. 😄

[donghaozhang]

I am glad it worked. swc variable is matrix in code which contains x y z information. you use 3d slicer mhd image and vtk to check your result.

[hanke580]

I really appreciate it! Thank you!
The code in this project is written really good!

[lsqshr]

@hanke580 thanks for trying out. Pls let us know how it works for you so we could improve this repo.