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Make antsBrainExtraction.sh less sensitive to image size #1640

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merged 2 commits into from
Jan 2, 2024

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@cookpa cookpa commented Dec 20, 2023

Addressing #1638.

Updated N4, downsampling procedure to not smooth and downsample non-human or neonate images too much.

I exposed the antsAI search parameters to the user because I think they are harder to guess from the input compared to the downsampling. The defaults are unchanged.

Specifically,

 * Change resampling before antsAI from a fixed to a variable
   resolution. Smooth images by 4 voxels, then downsample to
   5x template spacing. Previously, we downsampled to 4mm with
   a large smoothing kernel.

 * Change N4 from fixed spline spacing (200) to a 1x1x1 mesh.

 * Allow antsAI search parameters to be set on the command line.
@cookpa cookpa merged commit e1239db into master Jan 2, 2024
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@cookpa cookpa deleted the antsbe_affine_init_scale branch January 2, 2024 15:07
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