---
name: "antsNeuroimagingBattery"
section: "1"
platform: "linux"
package: "ants"
version: "2.5.4+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/antsNeuroimagingBattery"
---

# antsNeuroimagingBattery(1)

part of ANTS registration suite

## NAME

antsNeuroimagingBattery - part of ANTS registration suite

## SYNOPSIS

**antsNeuroimagingBattery.pl**

## DESCRIPTION

antsNeuroimagngBattery align MR modalities to a common within-subject (and optional template) space

**--input-directory** where to look for modality images

**--output-directory** where output goes (where antsCorticalThickness output lives)

**--output-name** file prefix for outputs

**--anatomical** reference subject image (usually T1)

**--anatomical-mask** mask of anatomical image, should contain cerebrum, cerebellum, and brainstem

\## OPTIONAL INPUTS ###

**--template** template image

**--template-transform-name** basename of transforms from anatomical to template space (must be in output base dir)

**--template-labels** labels in template space

**--dti-flag** DIRNAME/fileflag/outid \[for example DTI/\_30dir\_dt.nii.gz/30dir for a file in DTI/\*\_30dir\_dt.nii.gz \]

**--pcasl-flag** DIRNAME/fileflag/outid

**--pasl-flag** DIRNAME/fileflag/outid

**--pasl-m0-flag** DIRNAME/fileflag/outid

**--bold-flag** DIRNAME/fileflag/outid

**--rsbold-flag** DIRNAME/fileflag/outid

**--mt-flag** DIRNAME/fileflag/outid

**--no-mt-flag** DIRNAME/fileflag/outid

**--temp-directory** DIRNAME

**--help**

**--info-only** look for inputs, output what is there, but don't process any data.

\## NOTES ##

Modality flags should only return one image, but you may provide multiple flags of a single type

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

If you call

**--dti-flag** DTI/dt

it will find both files and fail due to insufficient specification