Fix voxel_res propagation and function signature mismatches in slice registration pipeline

[Copilot]

Resolution (voxel_res) was only propagated through the first few pipeline steps. All STAGE1, STAGE2, and groupwise template generation calls silently defaulted to 1×1×1. Additionally, convert_ants_warp_to_deformation would crash at runtime due to a signature mismatch.

slice_registration_functions.py

• do_initial_translation_reg: Forward voxel_res and use_resolution_in_registration through to do_reg — both were accepted but silently dropped
• convert_ants_warp_to_deformation: Add reference_image param to signature — called with 3 args from groupwise_stack_optimization but defined with 2 (TypeError at runtime)
• groupwise_stack_optimization: Add scaling_factor and voxel_res to signature to match caller

run_slice_registration.py

• Add voxel_res=voxel_res to all 10 generate_stack_and_template calls that were missing it (STAGE1, STAGE2, groupwise)
• Pass voxel_res to groupwise_stack_optimization
• Fix executor.submit() for initial translation — was executor.submit(fn(...)) (immediate call, serial) instead of executor.submit(fn, ...) (deferred, parallel):

# Before: calls fn immediately, submits return value
executor.submit(do_initial_translation_reg(sources, targets, ...))

# After: submits fn for parallel execution
executor.submit(do_initial_translation_reg, sources, targets, ...)

Original prompt

the recent changes to make the functions fine are of resolution only partly work in slice_registration_functions.py. check that all output files and stacks will have the correct set resolution and fix where necessary under both of the conditions that the user sets in run_silce_registration. there may also be errors in the running script file, so please check that the inputs and outputs match for all the steps

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[steelec]

primarily surface level changes, should be good but will not affect current issues.