I want to use FLIRT to apply registration on T1w images.
But I am quite confused if FLIRT automatically transforms images to standard MNI152.
This is the command that I am familiar with. It should align all images with the reference image.
What about the MNI152?
flirt -in <input_image.nii> -ref <reference_image.nii> -out <output_image.nii>
flirt does not automatically align to MNI. You need your reference image to be an MNI template T1 brain, e.g.,
May you guide me on how can I convert one image to MNI152?
MNI is a brain template that is distributed with some softwares, including FSL (see the path relative to
$FSLDIR in my last reply). You can align your input image to MNI space with commands such as