ANTSNEUROIMAGINGBATTERY(1)

📦
version 2.6.4 · 2 versions
, in ubuntu resolute

✨ ANTSNEUROIMAGINGBATTERY(1) ✨

bestie, this is the manual page for antsNeuroimagingBattery, filed under User Commands 🎀 let's get into it 💅

🦋 NAME 🦋

antsNeuroimagingBattery, part of the ANTS registration suite 🦋

🌸 SYNOPSIS 🌸

antsNeuroimagingBattery.pl

🧚 DESCRIPTION 🧚

okay so antsNeuroimagngBattery is literally the one that lines up MR modalities to a common within-subject space (and an optional template space too) ✨ here's the lineup:

  • --input-directory — where it goes looking for the modality images 🔍
  • --output-directory — where the output goes. this is where the antsCorticalThickness output lives 🧠
  • --output-name — the file prefix for all your outputs 🏷️
  • --anatomical — the reference subject image, usually T1 🧠👑
  • --anatomical-mask — the mask for the anatomical image. it should contain the cerebrum, cerebellum, and brainstem 🫶

✨ OPTIONAL INPUTS ✨

these are the extras, and they're giving main character energy 💖

  • --template — the template image 🌈
  • --template-transform-name — the basename of the transforms from anatomical to template space. these have to live in the output base dir ⚠️
  • --template-labels — the labels in template space 🏷️
  • --dti-flag DIRNAME/fileflag/outid — ngl the example is so helpful: DTI/_30dir_dt.nii.gz/30dir grabs a file in DTI/*_30dir_dt.nii.gz 🧩
  • --pcasl-flag DIRNAME/fileflag/outid — same flag format, pCASL edition 🍓
  • --pasl-flag DIRNAME/fileflag/outid — same format, PASL edition 🌸
  • --pasl-m0-flag DIRNAME/fileflag/outid — same format, PASL M0 edition 🦋
  • --bold-flag DIRNAME/fileflag/outid — BOLD, same format 🔥
  • --rsbold-flag DIRNAME/fileflag/outid — resting-state BOLD, same format 🧘‍♀️
  • --mt-flag DIRNAME/fileflag/outid — MT, same format 💜
  • --no-mt-flag DIRNAME/fileflag/outid — no-MT, same format 🙈
  • --temp-directory DIRNAME — takes a DIRNAME 🗂️
  • --help — the help one 🆘
  • --info-only — looks for inputs and outputs what's there, but doesn't process any data 👀

📝 NOTES 📝

okay listen, notes are where the real tea is ☕

Modality flags should only return one image 🖼️ but you can give multiple flags of a single type, periodt 💅

if you have the files DTI/name_12dir_dt.nii.gz & DTI/name_30dir_dt.nii.gz, you should call:

--dti-flag DTI/12dir_dt --DTI/30dir_dt

but if you call:

--dti-flag DTI/dt
bestie, this one is a trap 💀 it'll find both files and then fail because the specification isn't specific enough 😭

🎀 Bye bestie 🎀

this page is for version antsNeuroimagingBattery 2.6.4..., dated December 2025 🌈 and it's filed under ANTSNEUROIMAGINGBATTERY(1) in the User Commands section 💖 you're welcome, you're so welcome 🫶✨

📦 where this page comes from