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