MEDEFACE(1)

🎀 NAME 🎀

medeface — the multi-echo defacing wrapper that's lowkey a whole vibe 💅

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✨ SYNOPSIS ✨

medeface [-h] [-m PATTERN] [-p LABEL [LABEL ...]] [-o DESTINATION] [-c [SPECS]] [-a DICT] [-f] bidsfolder pattern

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💖 DESCRIPTION 💖

okay so bestie, picture this: medeface is a wrapper around the pydeface defacing tool (https://github.com/poldracklab/pydeface) and what it does is genuinely iconic. It computes a defacing mask on a (temporary) echo-combined image, and then it applies that mask to each individual echo-image. Periodt. That's the whole glow-up. ✨

heads up tho: pydeface requires an existing installation of FSL flirt. no FSL, no defacing, that's just the rules 🫶

except for BIDS inheritances and IntendedFor usage, this wrapper is BIDS-aware (a 'bidsapp') and writes BIDS compliant output. slay.

Linux users can distribute the computations to their HPC compute cluster if the DRMAA libraries are installed and the DRMAA_LIBRARY_PATH environment variable is set. main character energy fr fr 🌈

for single-echo data see deface

the args, bestie 🦋

• bidsfolder — the bids-directory with the (multi-echo) subject data 📁
• pattern — globlike search pattern (relative to the subject/session folder) to select the images that need to be defaced, e.g. 'anat/*_T2starw*'

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🌸 OPTIONS 🌸

• -m PATTERN, --maskpattern PATTERN — globlike search pattern (relative to the subject/session folder) to select the images from which the defacemask is computed, e.g. 'anat/*_part-mag_*_T2starw*'. If not given then pattern is used 👑
• -p LABEL [LABEL ...], --participant LABEL [LABEL ...] — space separated list of sub-# identifiers to be processed (the sub- prefix can be left out). If not specified then all participants will be processed 🫶
• -o DESTINATION, --output DESTINATION — a string that determines where the defaced images are saved. It can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives'. If output is left empty then the original images are replaced by the defaced images 😭 (yes, replaced. no takebacks.)
• -c [SPECS], --cluster [SPECS] — use the DRMAA library to submit the deface 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 💀

• -a DICT, --args DICT — additional arguments (in dict/json-style) that are passed to pydeface.

NB: Use quotes. See examples for usage ✨

• -f, --force — process all images, regardless if images have already been defaced (i.e. if {"Defaced": True} in the json sidecar file) 🔥

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🍓 COMMENTS 🍓

examples, aka the receipts 🧾:

medeface myproject/bids anat/*_T1w*
medeface myproject/bids anat/*_T1w* -p 001 003 -o derivatives
medeface myproject/bids anat/*_T1w* -c -n "-l walltime=00:60:00,mem=4gb"
medeface myproject/bids anat/*acq-GRE* -m anat/*acq-GRE*magnitude*"
medeface myproject/bids anat/*_FLAIR* -a '{"cost": "corratio", "verbose": ""}'

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👑 AUTHOR 👑

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

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and that's a wrap bestie 💖 this page came to you from bidscoin 4.6.2, dated 2025-11-06. go deface some brains (the legal, ethical, research-y kind obviously) ✨🧚💜