How to use FLIRT for Image Alignment and MNI152

1

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>
2

Hi @Yasmine,

flirt does not automatically align to MNI. You need your reference image to be an MNI template T1 brain, e.g., $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz.

Best,
Steven

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4

May you guide me on how can I convert one image to MNI152?

5

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 flirt.

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6

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT/UserGuide#Example_uses

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