Jesper would need to confirm it, but the Jacobian obtained with FNIRT does *not* take into account the affine (initial) part of the registration. So you would need to get the scaling factor(s) using avscale on the corresponding flirt matrix.
--- En date de : Mer 5.8.09, roberto toro <[log in to unmask]> a écrit :
> De: roberto toro <[log in to unmask]>
> Objet: [FSL] Jacobian in FNIRT
> À: [log in to unmask]
> Date: Mercredi 5 Août 2009, 16h56
> I have an ROI defined in MNI152 space, and I would like to
> measure its
> volume in native space using the jacobian volume produced
> by FNIRT
> with the --jout option. But does the jacobian include the
> scaling present in the affine matrix or I have to add it
> (multiply it
> in fact...)?
> If for example, the affine matrix changes the orientation
> but also the
> size of the input brain, do I have to add this scaling to
> the values
> of the jacobian at each voxel?
> thanks in advance!