Update README and scripts for refactoring and enhanced functionality

- Updated the `README.md` to reflect changes in script usage, specifically changing the command example to use `nii_to_df.py`.
- Added a new section on repository structure in `README.md` for better navigation and understanding.
- Included Python version compatibility note in `requirements.txt`, specifying the use of Python <= 3.12.
- Updated `spatial_normalization_mni152.py`:
  - Modified logging to output filenames of the `'*bold.nii'` files being processed.
  - Changed the behavior of `apply_affine_transformation` to return the normalized image without saving.
  - Implemented saving the affine transformed image in `main` function, enhancing data processing workflow.