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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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use Vlad's Scipy-based xfmavg #385

Closed bcdarwin closed 5 years ago

bcdarwin commented 5 years ago

... better numerical properties and gets rid of the annoying octave dependency (which is missing in Vlad's singularity containers).

I think this is still Python2-based unfortunately so it might be hard to support all users out of the box despite @nzxwang's work on running stages inside modified environments.

gdevenyi commented 5 years ago

Have you tried AverageAffineTransform AverageAffineTransformNoRigid from ANTs (with MINC transform support enabled?)

bcdarwin commented 5 years ago

Haven't tried. Note that Pydpiper also needs to average nonlinear transforms when run with '--registration-strategy=pairwise' or ...=pairwise_and_build_model.

gdevenyi commented 5 years ago

Ah, in the case of ANTs, affines and nonlinear are always separated, so they use AverageImages to just average deformation fields.

bcdarwin commented 5 years ago

That would work for us too in this particular instance.

gdevenyi commented 5 years ago

Options :+1:

bcdarwin commented 5 years ago

minc2_simple works with Python 3, so what's needed is slight cleanup of the script and changing the setup file to actually install it.