In the General ANTs 3D slicer extension I noticed something rather odd. I can take one of the default parameter presets, say “QuickSyn”, change nothing, and click “save as preset”. The new .json preset saves in the correct folder, but comparing this file with the original shows one key difference:…

The meaning of the parameter values for -2 and -1 are: -2: use no initialization transform, i.e. assume that the images are already nearly aligned -1: use the transform from a supplied transform node as the starting point for registration This does not appear to be documented anywhere, but I sort…

[image] sulli419: so I would actually like there to be no initial transform. Is there a value for this, blank, or maybe just delete the command entirely from the .json file? If you don’t need the initial transform, then just delete it. It is not a mandatory field to specify.

There are still cases where this initial transform feature might be useful for me, so I tried to see if the values change anything using a dummy comfiguration that should’t move my image other than the this initial transform, but it doesn’t seem to do anything. Can anyone get this to work? Also, s…

[image] mikebind: Load a preset like QuickSyN. Change the initialization feature to something else and then change it back to what you want. Save as a new preset Thanks. As far as I can tell the intialization feature can only be changed in the .json file not the GUI, so how to attempt this?…

In the GUI, you set it here: [image]

Oh funny. I had been ignoring that menu because I thought it was only for loading in custom intial transform files. If I change the values in the GUI it now has the expected consequeces on the registration. Interestingly though, no matter how many times I change it, when I save it in the GUI it w…

[image] mikebind: The meaning of the parameter values for -2 and -1 are: -2: use no initialization transform, i.e. assume that the images are already nearly aligned -1: use the transform from a supplied transform node as the starting point for registration This does not appear to be documente…

Yes, it feels like there is perhaps some confusion within the module about whether it conceptually considers the intitialization transform selection to be part of a preset or not. It includes a section with the setting in a saved preset, but it sounds like it doesn’t properly save or reload it, ins…

Saving parameter preset in ANTs extension changes initialization value

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mikebind (Mike Bindschadler) February 2, 2026, 6:45pm 6

In the GUI, you set it here:

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Saving parameter preset in ANTs extension changes initialization value

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