Restore qform_code on NIFTI_NORDIC output NIfTIs#28
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MATLAB's niftiwrite drops qform_code on output (sets it to 0), even when the input has a valid qform. Downstream AFNI tools prefer qform over sform and fall back to identity-voxel-space when qform_code=0, silently misaligning oblique data. Add a small helper that patches the qform_code and qform parameters at the documented NIfTI-1 header byte offsets after each niftiwrite call. Voxel data is not touched. No new dependencies (base MATLAB only). Fixes SteenMoeller#27
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Fixes #27
Summary
niftiwriteignoresinfo.raw.qform_code/quatern_*/qoffset_*on the write path, so every NIFTI_NORDIC output ends up withqform_code = 0. AFNI tools (which prefer qform over sform) then read the output as identity-voxel-space, silently misaligning oblique data with paired fieldmaps and crashing fMRIPrep's PEPOLAR SDC workflow on strongly-oblique acquisitions. See # for the full bug analysis and reproducer.What this PR changes
restore_qform_from_source(target_file, source_info, is_compressed)at the end ofNIFTI_NORDIC.m.niftiwriteinvocations (gfactor write, complex-mode magn write, complex-mode phase write, main output write).The helper writes
qform_code,quatern_b/c/d,qoffset_x/y/z, andpixdim[0](qfac) at their documented NIfTI-1 header byte offsets. The voxel data block is never opened..nii.gzoutputs are transparently gunzipped, patched, and re-gzipped.No new dependencies — uses only
fopen/fwrite/gzip/gunzipfrom base MATLAB.Verification
On a synthetic oblique input (
qform_code = 1, 45° rotation), before this PR:mag.nii.gzNORDIC_mag.nii.gzAfter this PR, the output's qform matches the input's bit-for-bit.
Full reproducer in the linked issue.
Notes
NIFTI_NORDIC.m.NORDIC.mmay have similarniftiwritecall sites; happy to extend the patch if you confirm.save_untouch_niifrom Jimmy Shen's NIfTI Tools, which would preserve qform natively — but that adds an external dependency, which I assumed you'd want to avoid).