Dear Joep,

I am afraid I didn’t include such an option specifically. In general the exact value of the cost-function is of limited value.

You can get something like what you want by supplying the estimated field as --inwarp and the estimated intensity mapping as --intin and then running fnirt with a single iteration, a --lambda and
--biaslambda of 0, a --subsamp=1 and specify the -v option. I _think_ that will display what you are after.

Jesper

On 3 Oct 2016, at 12:21, Kamps, J.J.W. <[log in to unmask]> wrote:

Dear FSL users,
 
Using FLIRT, it is possible to calculate the cost function value with the command:

flirt -in inpimage -ref refimage -schedule $FSLDIR/etc/flirtsch/measurecost1.sch -init inp2ref.mat
 
Is there a similar way to do this for warp fields calculated with FNIRT?
 
Thanks in advance.
 
Joep