Converting coordinates in native space to MNI space using FSL

1

Hi there, I have coordinates in native space that I’d like to convert to coordinates in MNI space. I’m using fsl’s flirt and img2imgcoord to accomplish this:

flirt -in stripped_brain_restore.nii.gz -ref ./mni_ref_image.nii.gz -out ./final_registered_image.nii.gz -omat ./native_to_mni_python.mat

img2imgcoord -src ./stripped_brain_restore.nii.gz -dest ./mni_ref_image.nii.gz -mm -xfm ./native_to_mni_python.mat coordinates.txt

However, I’ve read the FSL uses an internal coordinates system that differs from the NIFTI coordinate system (via JISCMail - FSL Archives). I’m looking for NIFTI coordinates; does img2imgcoord produce NIFTI coordinates, or coordinates in FSL’s internal coordinate system?

If img2imgcoord produces coordinates in FSL’s internal coordinate system, is it possible to produce coordinates in NIFTI space using FSL commands? Thank you!

2

Hi @swwalsh1, the -mm option causes img2imgcoord to expect NIFTI coordinates (w.r.t. the source image) as its input, and to produce NIFTI coordinates (w.r.t. the reference image) as its output.