SPEC2NII-JMRUI(1)

💖 SPEC2NII-JMRUI 💖

okay bestie, gather round, because this is spec2nii jmrui — the little glow-up machine that takes your jMRUI files (text or binary, she's versatile 💅) and turns them into the good stuff. it's a User Command. it's iconic. let's go 🦋

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✨ SYNOPSIS ✨

spec2nii jmrui [-h] [-a FILE] [-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

like, that's the whole vibe right there. every flag, every arg, all of it 🎀

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🌸 OPTIONS 🌸

👑 POSITIONAL ARGUMENTS

• file — the file you want converted. the main character, literally. give her the file. 🫶

💖 OPTIONAL ARGUMENTS

• -h, --help — shows you a help message and then dips. classic.
• -a FILE, --affine FILE — the NIfTI affine file. you're handing over the affine, bestie.
• -j, --json — makes a json sidecar. yes, a little companion file. she comes with a friend now. ✨
• -f FILEOUT, --fileout FILEOUT — the base name for your output file. and if you don't say anything? it just defaults to the input file name. she's low-maintenance like that.
• -o OUTDIR, --outdir OUTDIR — where the output goes. and if you say nothing, the default is . (which is just "right here", iykyk).
• --nifti1 — no description given, she's just standing there, being mysterious 💀 but she's real and she's in the list so we keep her.
• --override_nucleus OVERRIDE_NUCLEUS [OVERRIDE_NUCLEUS ...] — overrides the ResonantNucleus field with whatever input(s) you throw at it. e.g. '2H'. give it as many as you want, she's not judging. 🌈
• --override_frequency OVERRIDE_FREQUENCY [OVERRIDE_FREQUENCY ...] — overrides the SpectrometerFrequency field with your input(s). heads up, the input is in MHz. multiple inputs? slay, go off. ⭐
• --override_dwelltime OVERRIDE_DWELLTIME — overrides the dwell time field with your input. and the input is in seconds, bestie, don't forget. 🍓
• --anon — creates the file without sensitive metadata. so if you're shy about your data, this is your girl. and if you want even more control over the anonymising, go use spec2nii-anon(1) instead. 🧚
• --verbose — no description here either, she's just loud and proud 💜 she's in the list, that's all we know.

ngl, keep --anon in mind if there's anything in your headers you'd rather not share with the whole group chat. that's not a vibe, that's a whole identity. 🙈

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🌈 SEE ALSO 🌈

• spec2nii(1)

and the whole extended fam, because we don't gatekeep:

• 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-raw(1), spec2nii-bruker(1), spec2nii-varian(1), spec2nii-anon(1), spec2nii-dump(1), spec2nii-extract(1), spec2nii-insert(1), spec2nii-clean(1)

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and that's the page, periodt. 💅 this one's dated April 2026, and yeah, she's the spec2nii-jmrui(1) page, so if you forget everything else, just remember: convert your jMRUI files, read your flags, and stay hydrated. 🎀💖✨