Add Support for LTA IO and conversion

[m-reuter]

Adds Support for:

• xfm
• register.dat
• fslmat (FSL flirt)
• ITK/ANTs txt and ANTs mat
• NiftiReg
• Afni

Note, the implementation follow how we did this in FreeSurfer, however real tests with respect to some of these tools have not been performed yet. So some of this is still experimental.

[Copilot]

Pull request overview

Adds broad linear-transform I/O + conversion support across several neuroimaging ecosystems by normalizing through NeuroReg’s internal LTA (RAS-to-RAS) representation, and expands CLI/docs/tests accordingly.

Changes:

• Adds new transform wrappers with read/write + to_lta/from_lta conversion: XFM, register.dat, FSL FLIRT .mat, ITK/ANTs .tfm, ANTs GenericAffine .mat, AFNI affine text, NiftyReg affine text.
• Extends lta CLI with a new convert subcommand (format inference + overrides, geometry requirements, metadata passthrough).
• Consolidates and expands tests into tests/test_lta.py, and updates API/CLI documentation + README.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_lta_diff.py	Removes older LTA diff-focused test suite (superseded by consolidated tests).
tests/test_lta.py	Adds comprehensive tests for LTA + new transform formats and CLI convert/diff/invert/concat behavior.
neuroreg/transforms/lta.py	Adds top-level subject/fscale metadata handling and propagation through invert/concat; updates read/write.
neuroreg/transforms/xfm.py	Implements MNI/MINC .xfm parsing, path inference from comments, and LTA conversion.
neuroreg/transforms/regdat.py	Implements FreeSurfer register.dat I/O and LTA conversion using tkregister geometry conventions.
neuroreg/transforms/fsl.py	Implements FSL FLIRT .mat I/O and LTA conversion (geometry-dependent; NIfTI convention handling).
neuroreg/transforms/itk.py	Implements ITK/ANTs affine text .tfm I/O and LTA conversion (LPS↔RAS + inversion semantics).
neuroreg/transforms/antsmat.py	Implements experimental ANTs/ITK Matlab affine (*GenericAffine.mat) I/O and LTA conversion.
neuroreg/transforms/afni.py	Implements experimental AFNI affine text parsing/writing and LTA conversion (LPS↔RAS).
neuroreg/transforms/niftyreg.py	Implements NiftyReg affine text I/O and LTA conversion (stored inverse convention).
neuroreg/transforms/init.py	Exposes new transform wrappers via package imports and __all__.
neuroreg/cli/lta.py	Adds convert subcommand, format inference, and conversion read/write plumbing.
doc/cli/index.rst	Documents lta convert usage and examples.
doc/api/transforms.rst	Adds API docs for the new transform wrapper classes.
doc/api/cli.rst	Adds argparse-generated docs section for lta convert.
README.md	Updates CLI overview and adds detailed lta convert documentation + examples.

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