DEFACE(1)

📦
version 4.6.2 · 2 versions
, in fedora 43

💖 DEFACE(1) 💖

okay bestie, welcome to the deface page — it's a manual page, it lives in section 1 of the Generated Python Manual, and it's about to become your new personality. grab a snack, we're doing this 🍓

✨ NAME ✨

deface — the girl who removes faces from neuroimaging data and does it flawlessly, no cap.

🎀 SYNOPSIS 🎀

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

that's the whole summoning spell. yes it's long. yes it ate. 💅

🦋 DESCRIPTION 🦋

So basically, deface is a wrapper around the pydeface defacing tool — that's over at https://github.com/poldracklab/pydeface — and lowkey, it's doing a lot of heavy lifting for you. Heads up though: Pydeface requires an existing installation of FSL flirt or it's just gonna sit there looking at you. 😭

Except for BIDS inheritances and IntendedFor usage, this wrapper is BIDS-aware (a 'bidsapp', iykyk) and writes BIDS compliant output. it's giving organized. it's giving reproducible. it's giving slay.

Linux girlies, listen: you can distribute the computations to your HPC compute cluster if the DRMAA libraries are installed and the DRMAA_LIBRARY_PATH environment variable is set. cluster era unlocked 🔥

For multi-echo data see medeface — that's a whole different queen, go read her page.

Here's the positional tea:

  • bidsfolder — the bids-directory with the subject data. it's the home base, the main character location 🏠
  • pattern — a globlike search pattern (relative to the subject/session folder) that picks which images need to be defaced, e.g. 'anat/*_T1w*'. very "select your fighters" energy ✨

💅 OPTIONS 💅

  • -p LABEL [LABEL ...], --participant LABEL [LABEL ...] — a space separated list of sub-# identifiers to process (the sub- prefix can be left out, we're chill like that). If you don't specify it, then all participants get processed. everyone's invited to the party 🫶
  • -o DESTINATION, --output DESTINATION — a string that decides where the defaced images get saved. It can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives'. And if output is left empty? then the original images are replaced by the defaced images. ⚠️ no takebacks, bestie — that's the real deal.
  • -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 below for the vibe ✨
  • -a DICT, --args DICT — additional arguments (in dict/json-style) that get passed to pydeface. NB: Use quotes. See examples for usage. fr fr, quote it.
  • -f, --force — deface all images, regardless if they have already been defaced (i.e. if {"Defaced": True} in the json sidecar file). she said do it again. 💀

🌈 COMMENTS 🌈

examples, aka the group chat screenshots:

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

look at her go 😭👑

👑 AUTHOR 👑

Marcel Zwiers <m.zwiers@donders.ru.nl> — the icon, the legend, the moment.

and that's the whole page, bestie!! 💜 this is from bidscoin 4.6.2, dated 2025-11-06, so if you're quoting it in your thesis, cite her right. go deface some brains responsibly. mwah 🎀✨

📦 where this page comes from