153 bug defaultvalue for padding when registering without skull stripping seems to be off

[MarcelRosier]

The issue arises when the registrations lead to out-of-view voxels that will be filled with a default value (by default, 0). However, if the image is not normalised, 0 does not correspond to the background channel, leading to artefacts.
As a solution, we set the default padding value to the minimum of the moving image - this seems to fix the issue. We will have to monitor if this causes issues elsewhere.

As of now, this fix is only implemented for ANTs and niftyreg.

[Copilot]

Pull Request Overview

This PR fixes a bug where default padding values during image registration were causing artifacts when images weren't normalized. The fix sets the default padding value to the minimum value of the moving image instead of using 0, which better represents the background when working with non-normalized images.

• Updated ANTs and NiftyReg registration methods to use minimum image value as default padding
• Modified shell scripts to accept and use the new padding value parameter
• Added automatic padding value calculation based on moving image minimum

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
brainles_preprocessing/registration/ANTs/ANTs.py	Added automatic defaultvalue setting to minimum of moving image and refactored to use transform method
brainles_preprocessing/registration/niftyreg/niftyreg.py	Added padding value calculation and parameter passing to shell scripts
brainles_preprocessing/registration/niftyreg/niftyreg_scripts/rigid_reg.sh	Updated to accept and use padding value parameter
brainles_preprocessing/registration/niftyreg/niftyreg_scripts/transform.sh	Updated to accept and use padding value parameter

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