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