# NIfTI Header Support

When trx-cpp is built with `TRX_ENABLE_NIFTI=ON`, the optional NIfTI I/O
module can read qform/sform affines from `.nii`, `.hdr`, or `.nii.gz`
files and embed them in the TRX `VOXEL_TO_RASMM` header field.

This is primarily useful when the TRX file must interoperate with the
`.trk` (TrackVis) format, which stores coordinates in voxel space and
relies on the NIfTI header for the voxel-to-world transform.

## Attach a NIfTI affine to a TRX file

```cpp
#include <trx/nifti_io.h>
#include <trx/trx.h>

Eigen::Matrix4f affine = trx::read_nifti_voxel_to_rasmm("reference.nii.gz");

auto trx = trx::load<float>("tracks.trx");
trx->set_voxel_to_rasmm(affine);
trx->save("tracks_with_ref.trx");
trx->close();
```

## Notes

- The qform is preferred when present. If only the sform is available, it is
  orthogonalized to a qform-equivalent matrix, consistent with ITK's NIfTI
  handling.
- The qform/sform logic is adapted from nibabel's MIT-licensed implementation
  (see `third_party/nibabel/LICENSE`).
- zlib must be discoverable by CMake to build `.nii.gz` decompression
  support.

## Enable at build time

```bash
cmake -S . -B build -DTRX_ENABLE_NIFTI=ON
cmake --build build
```