SPEC2NII-CLEAN(1)

💖 SPEC2NII-CLEAN — the glow-up page 💖

okay bestie, listen. this is spec2nii-clean, a lil User Command from the spec2nii fam, and her whole job is fixing up the messy invalid fields chillin' in a NIfTI-MRS header. like, she does a vibe check on your header and edits the stuff that's giving nothing. no cap. 🎀

✨ SYNOPSIS ✨

spec2nii clean [-h] [-j] [-f FILEOUT] [-o OUTDIR] [--nifti1]
[--override_nucleus OVERRIDE_NUCLEUS [OVERRIDE_NUCLEUS ...]]
[--override_frequency OVERRIDE_FREQUENCY [OVERRIDE_FREQUENCY ...]]
[--override_dwelltime OVERRIDE_DWELLTIME] [--anon] [--verbose] file

🌸 OPTIONS 🌸

🫶 POSITIONAL ARGUMENTS

• file — your NIfTI-MRS file. the main character. hand her over. 💅

🦋 OPTIONAL ARGUMENTS

• -h, --help — pops up a help message and dips. classic.
• -j, --json — makes a json sidecar. sidecar bestie, riding along. ✨
• -f FILEOUT, --fileout FILEOUT — sets the output file base name. default is the input file name, so if you don't say anything she just reuses your name (iconic, honestly).
• -o OUTDIR, --outdir OUTDIR — where the output goes. default is . — aka right here, right now, no travel.
• --nifti1 — that's it. that's the whole option. no description in the source, so no notes from me, fr fr. 🙈
• --override_nucleus OVERRIDE_NUCLEUS [OVERRIDE_NUCLEUS ...] — overrides the ResonantNucleus field with your input(s). e.g. ‘2H’. give her one, or give her a whole lil lineup.
• --override_frequency OVERRIDE_FREQUENCY [OVERRIDE_FREQUENCY ...] — overrides the SpectrometerFrequency field with your input(s). heads up: the input is in MHz. 📻
• --override_dwelltime OVERRIDE_DWELLTIME — overrides the dwell time field with your input. input is in seconds. tick tock. ⏱️
• --anon — creates a file with no sensitive metadata. privacy slay. and lowkey if you want greater control over the anon-ing, go use spec2nii-anon(1) instead, she's the specialist. 👑
• --verbose — that's all she wrote. literally. no description in the original, so I'm not gonna make one up. 💀

ngl, a couple of these options are giving "mystery box" because the original manpage didn't describe them. I'm keeping it honest and not guessing — the facts stay the facts, periodt.

🌈 SEE ALSO 🌈

• spec2nii(1)

and the whole squad, all together now:

• spec2nii-auto(1), spec2nii-twix(1), spec2nii-dicom(1), spec2nii-rda(1), spec2nii-uih(1), spec2nii-philips(1), spec2nii-philips_dl(1), spec2nii-philips_dcm(1), spec2nii-ge(1), spec2nii-text(1), spec2nii-jmrui(1), spec2nii-raw(1), spec2nii-bruker(1), spec2nii-varian(1), spec2nii-anon(1), spec2nii-dump(1), spec2nii-extract(1), spec2nii-insert(1)

and that's the whole page, bestie. 🫶 this one's a User Command, dated April 2026, and the source is SPEC2NII-CLEAN(1) — so go clean that header, she's been waiting. 💖✨