Editing landmarks between auto3DGM phases

Hi, all another newbie question here. I am using auto3DGM to landmark some turtle hemiskulls, and I do not need landmarks on the inside of the cranium. Currently my solution is to run auto3DGM as is and then go through the generated landmarks and generate a list to remove for the GPA, which is quite tedious to do for 1000+ landmarks in the markup module. I am being helped with my issues on this front elsewhere on this forum, but I have thought of another possibility though I don’t think there is a way to implement it.

I have noticed that there are buttons to separate the phases of auto3DGM, which I assume are there to help organize the computing time. Is there a way to run the module through phase 1, remove landmarks that are not relevant, and then feed those trimmed landmarks into phase 2 ? This would save on computing time and give me much more control over the number of landmarks I am using. There is not currently a way to add landmark files in the module, so I’m assuming it will have to be forced via script. I’m not sure what is possible.

Thanks for any ideas you may provide,


I am not sure if any of the auto3Dgm developers are tracking the forum. You might get faster response if you contact them directly.

Meanwhile, did you try using the MarkupEditor in the SlicerMorph to choose your landmarks? At least it might help you with the generating the list to remove for GPA a bit?

Yes, that is what I have been using the generate the list in the other thread, and why I made the switch to Slicer over R, since the markup editor is so easy to use!

I have contacted them, but was hoping other members may have some experience!

Thank you for all your help!

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