SKULLSTRIP(1)

💀✨ SKULLSTRIP ✨💀

ok so this is the skullstrip page from the Generated Python Manual, and bestie, it's giving "delete the skull, keep the brain" energy and honestly? iconic. 💅

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🌸 SYNOPSIS 🌸

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

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🧠 DESCRIPTION 🧠

It's a lil wrapper around FreeSurfer's synthstrip skull stripping tool (<https://surfer.nmr.mgh.harvard.edu/docs/synthstrip>). Not a link in the "click me" sense but you get it, that's the docs URL, go read it.

Except for BIDS inheritances, this wrapper is BIDS-aware (a bidsapp) and writes BIDS compliant output. no cap, it plays by the BIDS rules. 🎀

The corresponding brain mask gets saved in the bids/derivatives/synthstrip folder. that's where the mask lives now, periodt.

Assumes the installation of FreeSurfer v7.3.2 or higher — like, if you're on an older one, this is not the vibe, upgrade bestie. 🫶

bidsfolder The bids-directory with the subject data. it's the folder, it's got the subjects, that's the whole thing. 🌈

pattern Globlike search pattern (relative to the subject/session folder) to select the (3D) images that need to be skullstripped, e.g. 'anat/*_T1w*'. so like, you glob it, it picks the pics, we strip the skulls. ✨

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💅 OPTIONS 💅

• -p LABEL [LABEL ...], --participant LABEL [LABEL ...] — Space separated list of sub-# identifiers to be processed (the sub- prefix can be left out, so you can be lazy, it's fine 💖). If not specified then all participants will be processed. everyone's getting the treatment. 👑
• -m PATTERN, --masked PATTERN — Globlike search pattern (relative to the subject/session folder) to select additional (3D/4D) images from the same space that need to be masked with the same mask, e.g. 'fmap/*_phasediff'. same mask, more images, efficient queen behaviour. 🦋 NB: This option can only be used if pattern yields a single file per session. one file per session or it simply does not work, no exceptions.
• -o DESTINATION [DESTINATION ...], --output DESTINATION [DESTINATION ...] — One or two output strings that determine where the skullstripped + additional masked images are saved. Each output string can be the name of a BIDS datatype folder, such as 'anat', or of the derivatives folder, i.e. 'derivatives' (default). ✨ If the output string is the same as the datatype then the original images are replaced by the skullstripped images. ⚠️ like, replaced replaced. heads up.
• -f, --force — Process images, regardless whether images have already been skullstripped (i.e. if {'SkullStripped': True} in the json sidecar file). it doesn't care that you already did it, it's doing it again. main character energy. 🔥
• -a ARGS, --args ARGS — Additional arguments that are passed to synthstrip. NB: Use quotes and include at least one space character to prevent premature parsing. quotes + a space, bestie, or the parser gets confused and we all cry. 😭
• -c [SPECS], --cluster [SPECS] — Use the DRMAA library to submit the skullstrip 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. same deal as before: quotes, space, or chaos. 💀

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🍓 COMMENTS 🍓

examples, aka the receipts:

skullstrip myproject/bids anat/*_T1w*
skullstrip myproject/bids anat/*_T1w* -p 001 003 -a " --no-csf"
skullstrip myproject/bids fmap/*_magnitude1* -m fmap/*_phasediff* -o
extra_data fmap
skullstrip myproject/bids fmap/*_acq-mylabel*_magnitude1* -m
fmap/*_acq-mylabel_* -o fmap

ok notice how in example two the -a value starts with a space inside the quotes? and in example three the -o line wraps onto extra_data fmap? that's the "include at least one space character" thing in action, don't @ me, that's just how it is. 🙈

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🌟 AUTHOR 🌟

Marcel Zwiers <m.zwiers@donders.ru.nl> — the legend who wrote this, respect. 💜

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and that's the whole page bestie!! 🎀 the footer said it's bidscoin 4.6.2 and it's dated 2025-11-06, so yeah, that's the version and the date, slay, go strip some skulls, you got this 💖🦋✨