SPEC2NII(1)

✨ spec2nii — the glow-up your spectroscopy data deserves ✨

okay bestie, listen. this is spec2nii(1), a User Commands situation, and it's literally the tool that takes your raw spectroscopy data and turns it into NIfTI format. no cap. 💖

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🌸 NAME 🌸

spec2nii — convert raw spectroscopy data to NIfTI format. that's it. that's the whole job. and it does it flawlessly. 💅

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🎀 SYNOPSIS 🎀

spec2nii [-h] [-v]
{auto,twix,dicom,rda,uih,philips,philips_dl,philips_dcm,ge,text,jmrui,raw,bruker,varian,anon,dump,extract,insert,clean} ...

so like, you pick a subcommand from that big gorgeous list, and then it does the thing. main character energy fr fr. ✨

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🦋 OPTIONS 🦋

💜 POSITIONAL ARGUMENTS 💜

these are the subcommands, one per data format (plus some extra little helpers at the end, iykyk):

• auto — bestie it just figures it out. Attempt automatic identification and conversion. 🪄
• twix — Convert from Siemens .dat twix format.
• dicom — Convert from Siemens DICOM format.
• rda — Convert from Siemens spectroscopy .rda format.
• uih — Convert from UIH DICOM format.
• philips — Convert from Philips spar/sdat format.
• philips_dl — Convert from Philips data/list format.
• philips_dcm — Convert from Philips DICOM format.
• ge — Convert from GE p-file format.
• text — Convert from plain text format. yes, just text. humble but iconic. 📝
• jmrui — Convert from jMRUI text or binary formats.
• raw — Convert from LCModel RAW text format.
• bruker — Convert from Bruker data format.
• varian — Convert from the Varian/OpenVnmrJ data format
• anon — Anonymise existing NIfTI-MRS file. privacy queen behavior 🕶️
• dump — Dump contents of headers from existing NIfTI-MRS file.
• extract — Generate json sidecar from existing NIfTI-MRS file.
• insert — Insert json formatted file into existing NIfTI-MRS file.
• clean — Update invalid fields in NIfTI-MRS header. little janitor moment 🧹

🌈 OPTIONAL ARGUMENTS 🌈

• -h, --help — Show a help message and exit. when in doubt, ask for help, that's growth bestie 🫶
• -V, --version — Show program's version number and exit.

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⭐ NOTES ⭐

if you use spec2nii(1), you gotta cite it. it's the rules. give credit where credit is due, periodt. 👑

the citation, exactly as written:

Clarke WT, Bell TK, Emir UE, Mikkelsen M, Oeltzschner G, Shamaei
A, Soher BJ, Wilson M.  NIfTI-MRS: A standard data format for
magnetic resonance spectroscopy.  Magn Reson Med. 2022.  doi:
10.1002/mrm.29418.

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💀 SEE ALSO 💀

the whole friend group, all here, all slaying:

• 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)
• spec2nii-clean(1)

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that's the whole page bestie!! 🦋 this one's stamped April 2026 and it's page SPEC2NII(1) of your manual, and honestly? she ate. go convert something. 💖✨🎀