ANTSASLPROCESSING(1)

🎀 ANTSASLPROCESSING(1) 🎀

okay so the manual name is antsASLProcessing and it's a User Command bestie 💅

✨ NAME ✨

antsASLProcessing - part of ANTS registration suite 🦋

🌈 DESCRIPTION 🌈

Okay so first things first, if the tools aren't on your path, it's giving error vibes 💀 You'll get one of these:

Cannot find antsRegistration.  Please \(re\)define $PATH in your environment.
Cannot find antsApplyTransforms.  Please \(re\)define $PATH in your environment.
Cannot find antsIntermodalityIntrasubject.sh script.  Please \(re\)define $PATH in your environment.

Now the main event 🔥 antsASLProcessing does ASL processing using ANTs tools. It assumes your T1 images were already preprocessed with antsCorticalThickness.sh, no cap. Here's the lineup of steps:

1. Calculation of average pCASL image.
2. Skull stripping of average pCASL image.
3. Registration of average pCASL image to T1 image.
4. (Robust) calculation of mean CBF.
5. Warping tissue priors and labels to ASL space.
6. Warping mean CBF image to template space for VBM analysis.

💅 Usage

Okay bestie, here's the full usage line in one go:

antsASLProcessing -a anatomical image (skull stripped) -p brain segmentation priors (C-style, e.g. priors%d.nii.gz) -g hard brain segmentation -x t1 brain mask -s raw pCASL image -e brain template -l template labels -t skull-stripped t1 to template transform prefix -o output prefix

🧚 Required arguments

• -a anatomical image (skull stripped) — your anatomical image, already skull stripped 🧠
• -p brain segmentation priors — C-style naming, e.g. priors%d.nii.gz 🎀
• -g hard brain segmentation — the hard brain segmentation 🌸
• -x t1 brain mask — your T1 brain mask 🦋
• -s raw pCASL image — the raw pCASL image 💜
• -e brain template — the brain template 👑
• -l template labels — the template labels ⭐
• -t skull-stripped t1 to template transform prefix — the prefix for the skull-stripped T1 to template transform 🫶
• -o output prefix — the prefix for your outputs 🍓

🌸 Optional arguments

• -b blood T1 value — defaults to 0.67 s^-1 💖
• -r robustness parameter — defaults to 0.95 🔥
• -h — print help and exit 🙈
• -n number of bootstrap samples — defaults to 20 ✨
• -c percent to sample per bootstrap run — defaults to 70 🌈
• -k — keep tmp files, including warps; defaults to false 🧚

Heads up bestie, -k takes lots of space to save, so only keep those tmp files if you really need them 💀

• -i — use inverse warps. Warps are assumed to go in the direction of subject to template.

If you're instead using template to subject warps (e.g. the brain segmentation prior warps from antsCorticalThickness.sh), use -i. It's a binary switch, so no arguments 💅

• -f bootstrap with replacement? — takes "false" or "true"; defaults to false 🦋

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Okay that's the whole page, bestie 💖 Footer deets: antsASLProcessing 2.6.4+dfsg, December 2025, ANTSASLPROCESSING(1) 🫶 Stay iconic 👑✨