What I want is to get a Jacobian determinant from MNI152.nii.gz to struc.nii.gz (see below for the details). I would like to calculate atrophy rate of a specific region obtained from one given FSL atlas. However, I do not want to change raw structural images (not like what others did).

I have a structure image (struc.nii.gz) and have normalized it to MNI152 space (let me call the template MNI152.nii.gz) with non-linear transformation. Thus, I have the corresponding warp coefficients (warp_in_MNI.nii.gz) and Jacobian field from struc.nii.gz to MNI152.nii.gz. It seems not difficult. I did the following steps:

1) invwarp --ref=struct --warp=warps_in_MNI --out=warps_in_struct

2) fnirtfileutils --in=warps_in_struct --ref=struct --jac=struc_jac

at this step I get this error "fnirtfileutils: Can presently only generate Jacobian from coefficient files"

This error indicates that warps_in_struct.nii.gz does not like the coefficients output (-cout) from flirt. Some information may be loss during this inverse step.

I do appreciate if someone could share some ideas to deal with that.

Thanks,

Liang

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Liang Wang, PhD
Neuroscience of Attention and Perception Laboratory
Princeton Neuroscience Institute
Princeton University
Princeton, NJ, 08540