BIDSCOINER(1)

💖 BIDSCOINER 💖

okay bestie, so this is bidscoiner — it lives in the bidscoin 4.6.2 era (dated 2025-11-06) and it is literally the moment your messy raw scan folder gets its glow-up ✨

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✨ NAME ✨

bidscoiner — your little conversion fairy that turns raw source data into a full-on BIDS baddie 🧚

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🎀 SYNOPSIS 🎀

bidscoiner [-h] [-p LABEL [LABEL ...]] [-b NAME] [-f] [-c [SPECS]]
sourcefolder bidsfolder

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🌸 DESCRIPTION 🌸

So here's the tea: bidscoiner "coins" your source datasets into NIfTI/json/tsv BIDS datasets, using the mapping info it finds in the bidsmap.yaml file. Periodt. 🫶

Before you run it, go edit that bidsmap to your needs with the bidseditor tool, or (re-)run the bidsmapper whenever you run into unexpected data. That's the vibe check.

You can run bidscoiner once all your data has been collected, OR run/re-run it whenever new data has been added to your source folder (assuming the scan protocol hasn't changed). Also — and this is lowkey iconic — if you delete a subject/session folder from the bidsfolder, it will simply be re-created from the sourcefolder the next time you run bidscoiner. It really said "not me being the backup plan" 😭💅

The bidscoiner uses plugins, as stored in the bidsmap['Options'], to do the actual work.

Provenance information, warnings and error messages are stored in the bidsfolder/code/bidscoin/bidscoiner.log file. So if something's acting up, that log is your main character. 📝

• sourcefolder — The study root folder containing the raw source data 🌱
• bidsfolder — The destination/output folder with the bids data 👑

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💅 OPTIONS 💅

• -p LABEL [LABEL ...], --participant LABEL [LABEL ...] — Space separated list of selected sub-# names/folders to be processed (the sub- prefix can be omitted). Otherwise all subjects in the sourcefolder will be processed. Pick your faves only 💖
• -b NAME, --bidsmap NAME — The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the base name (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml. That's the default bestie, no cap 🎀
• -f, --force — Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped. Yes, it's giving "we're doing this whether you like it or not" 🔥
• -c [SPECS], --cluster [SPECS] — Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster. You can add an opaque DRMAA argument with native specifications for your HPC resource manager. ⚡

NB: Use quotes and include at least one space character to prevent premature parsing — see examples. fr fr, the quoting matters 🫠

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🦋 COMMENTS 🦋

examples, aka the receipts:

bidscoiner myproject/raw myproject/bids
bidscoiner -f myproject/raw myproject/bids -p sub-009 sub-030
bidscoiner -f myproject/raw myproject/bids -c "--time=00:30:00
--mem=4000"

look at that cluster one go 👑 — quotes AND a space, exactly like we said. iykyk 💜

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⭐ AUTHOR ⭐

Marcel Zwiers <m.zwiers@donders.ru.nl> — the actual genius behind all this 🫶✨

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okay that's the whole page bestie, you ate it, now go coin some datasets 💅🌈

this was the bidscoiner page from the Generated Python Manual, hailing from bidscoin 4.6.2, dated 2025-11-06 — mwah, bye 👋💖