PARREC2NII(1)

💖 PARREC2NII 💖

okay so bestie, welcome to parrec2nii — she's a User Command, she lives in section 1 of the manual, and her whole entire job is turning PARREC images into NIfTI. that's it. that's the girl. 🎀

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✨ NAME ✨

parrec2nii — convert PARREC image to NIfTI

like literally the name says it. PAR/REC in, NIfTI out. no notes. 💅

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🌸 SYNOPSIS 🌸

parrec2nii [OPTIONS] <PAR files>

so you hand her some <PAR files> and a pile of options, and she does her thing. the options are the whole vibe, so let's get into it.

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🦋 DESCRIPTION 🦋

Code for PAR/REC to NIfTI converter command.

(that's the official description and honestly it's giving "just vibes, no words". she's a command. the description is a command. we move. 😭)

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👑 OPTIONS 👑

every single one, in order, no skips, no cuts. this is the whole menu and you're gonna read all of it because I said so. 💜

• --version — shows the program's version number and then dips. exit stage left. 🚪
• -h, --help — shows this exact help message and exits. your emergency contact when you're lost. 🫶
• -v, --verbose — "Make some noise." that's the official wording and honestly? iconic. she's chatty now. 🗣️
• -o OUTDIR, --output-dir=OUTDIR — where the NIfTI files go, bestie. the destination directory. Default: the current directory. 🏠
• -c, --compressed — whether to write compressed NIfTI files or not. yes/no, that's the whole deal. 🗜️
• -p, --permit-truncated — permits conversion of truncated recordings. ⚠️ heads up though: support for this is experimental, and the results must be checked afterward for validity. like, for real, check them. do not trust and just vibe. she said must. 😭
• -b, --bvs — outputs bvals/bvecs files in addition to the NIFTI image. extra files, extra love. 📦
• -d, --dwell-time — calculates the scan dwell time. and if you supply this, you should also supply the magnetic field strength using --field-strength (default 3). why? because the field strength is not encoded in the PAR/REC format, so she literally cannot know it without you telling her. the field strength must be supplied. no cap. 🧲
• --field-strength=FIELD_STRENGTH — the magnetic field strength of the recording. only needed for --dwell-time. (again: it must be supplied manually because it is not encoded in the PAR/REC format. she can't read minds, bestie.) ✨
• -i, --volume-info — exports .PAR volume labels corresponding to the fourth dimension of the data. the dimension info gets stored in CSV format, with the first row containing dimension labels and the subsequent rows (one per volume) holding the corresponding indices. and, important: only labels that vary along the 4th dimension are exported — e.g. for a single volume structural scan there are no dynamic labels and no output file will be created at all. so if nothing shows up, that's not a bug, that's the rules. 🙈
• --origin=ORIGIN — the reference point of the q-form transformation of the NIfTI image. if 'scanner', the (0,0,0) coordinates refer to the scanner's iso center. if 'fov', this coordinate is the center of the recorded volume (field of view). Default: 'scanner'. pick your center, main character energy only. 🎯
• --minmax=MINMAX — the minimum and maximum settings to be stored in the NIfTI header. if any of them is set to 'parse', the scaled data is scanned for the actual minimum and maximum. to bypass that potentially slow and memory intensive step (the data has to be scaled and fully loaded into memory, oof), you can provide fixed values as a space-separated pair, e.g. '5.4 120.4'. and yes — it's possible to set a fixed minimum and scan for the actual maximum, or the other way around. Default: 'parse parse'. 🍓
• --store-header — if set, all information from the PAR header is stored in an extension of the NIfTI file header. hoarding? no, archival. Default: off. 📚
• --scaling=SCALING — choose your data scaling setting. the PAR header defines two different data scaling settings: 'dv' (values displayed on console) and 'fp' (floating point values). you can pick either one, or disable scaling completely with 'off'. important note: neither method will actually scale the data — it just stores the corresponding settings in the NIfTI header. unless non-uniform scaling is used, in which case the data is stored in the file in scaled form. Default: 'dv'. 📐
• --keep-trace — do not discard the diagnostic Philips DTI trace volume, if it exists in the data. keep the little guy. 🥺
• --overwrite — overwrite the file if it exists. Default: False. 💥
• --strict-sort — use additional keys in determining the order to sort the slices within the .REC file. this may be necessary for more complicated scans with multiple echos, cardiac phases, ASL label states, etc. messy scan? she's got extra keys for that. 🔑🔑

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🌈 a lil sign-off 🌈

that's the whole page, bestie! this was parrec2nii version 5.4.2, dated June 2026, and it's filed under PARREC2NII(1). go convert something and slay. 💖✨🦋