Hi,
I'm trying to understand the file format of the deformation fields output by
fnirtfileutils. Based on the documentation my understanding is this.
1) the field file has the same geometry as the reference image.
2) the value at every voxel is a vector in R3, describing the displacement
(in mm) of that voxel. So a voxel at location p in the reference image
corresponds to the voxel at p + d in the moving image.
My question concerns the frame of reference for the moving and reference
images. I know that flirt does not use the nifti defined coordinate systems,
it instead uses an internal coord system in mm(
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=FSL&P=R93775&X=0E7A1860A6D859E991&Y=lbloy%40seas.upenn.edu
).
Is this also true of fnirt?
What I would like is to be able to output a displacement field were the
vectors are expressed in LPS, ie +x = Left, +y = Posterior etc. Any
suggestions on how to go about that?
Thanks in advance.
Luke
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