SPEC2NII-VARIAN(1)

🌸 SPEC2NII-VARIAN 🌸

okay bestie, welcome to the spec2nii-varian manual page 💖 this is one of the User Commands, and it's the little guy whose whole job is converting from the Varian/OpenVnmrJ data format. no cap. let's get into it 🦋

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✨ NAME ✨

spec2nii varian – convert from the Varian/OpenVnmrJ data format

like. that's it. that's the whole assignment and she ate 💅

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🎀 SYNOPSIS 🎀

spec2nii varian [-h] [-t6 TAG6] [-d] [-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

copy that exactly, do not freestyle, I am begging 🙈

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💜 OPTIONS 💜

🍓 POSITIONAL ARGUMENTS 🍓

• file — the path to the varian .fid directory, the one holding your procpar and fid files. that's where all the good stuff lives, periodt.

🌈 OPTIONAL ARGUMENTS 🌈

• -h, --help — shows a help message and then dips. iconic behavior honestly ✨
• -t6 TAG6, --tag6 TAG6 — lets you specify the dim 6 NIfTI MRS tag. the default is DIM_DYN 👑
• -d, --dump_headers — dumps the varian header info into a json header extension. (the manpage literally says "Dump Dump" here, and I refuse to edit her, she's perfect 💀)
• -j, --json — creates a json sidecar. sidecar bestie rights 🛵
• -f FILEOUT, --fileout FILEOUT — the output file base name. default = the input file name, so if you don't say anything she just keeps the name you gave her 🫶
• -o OUTDIR, --outdir OUTDIR — where the output goes. default = . (aka right here, in your current directory, lowkey cozy)
• --nifti1 — okay so. the original manpage lists this flag but gives it no description at all. no text, no nothing. I'm not gonna invent one, that's not the vibe 💀 it exists, that's what we know, moving on 🧚
• --override_nucleus OVERRIDE_NUCLEUS [OVERRIDE_NUCLEUS ...] — overrides the ResonantNucleus field with your input(s). e.g. '2H' 💫
• --override_frequency OVERRIDE_FREQUENCY [OVERRIDE_FREQUENCY ...] — overrides the SpectrometerFrequency field with your input(s). the input is in MHz 📻
• --override_dwelltime OVERRIDE_DWELLTIME — overrides the dwell time field with your input. the input is in seconds ⏱️
• --anon — creates a file with no sensitive metadata. if you want greater control over the anonymisation, use spec2nii-anon(1) instead, she's the specialist 💅
• --verbose — (no description in the original, so I'm not making one up — she's just there, being mysterious ✨)

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👀 SEE ALSO 👀

• spec2nii(1)

and the whole extended fam, go say hi:

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

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bestie reminder: every flag above does exactly what it says and nothing more. if the manpage didn't say it, I didn't say it either 🫶

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okay that's the whole page, we're done, go convert something gorgeous 💖 this one's dated April 2026 and comes to you from the SPEC2NII-VARIAN(1) era of the manual — stay hydrated, back up your data, and slay 🌈👑✨