Hi Onur,

The article was very helpful with the command lines, thank you. I have a few questions, hopefully you can answer them since you were able to work through the main pipeline.

1. What is the number you put for --label for SegPostProcess and GenParaMesh? For the given hippocampus tutorial data set, I noticed that if I put --label 1, the output is an empty image, and if I leave the --label out using the default value of 0, I actually get a volume image. However, when I apply --label 0 using the output binary file from SegPostProcess for GenParaMesh, an error occur.

2. For GenParaMesh, do you only get two mesh outputs: _para.meta and _surf.meta ?

3. In the article, for ParaToSPHARMMesh, they have filenames for flipTemplate and regTemplate. Where would I usually find the .coef and .meta file for those inputs?

Thank you,
Sylvia