I am trying to run the 3 steps of SPHARM-PDM separately using commandline options. I can see that SlicerSALT has a commandline option but this generates all the 3 steps together i.e. just like how you could run them in the software-GUI and also not all the parameter options are available here either (which I want to modify for my subjects). I see that all those parameter options (that I need) are available when you run the steps if you go to “shape creation” and then “advanced”. However, I believe that this only runs for one subject i.e. not as a batch in an automated fashion.
I was wondering if I could run many subjects as a batch from the commandline or may be from the software GUI but utilizing all the parameter options. Previously, we could use the SPHARM-PDM binary executables to run those steps one at a time. I am not sure if that is still an option now, assuming that the results of running SPHARM-PDM from SlicerSALT is not the same as the output generated from executing those binary files because the binary files may not be updated anymore.
I am stuck with my shape analysis for quite some time. Any help would be greatly appreciated!