Strange output when registering brain MRI to CT scan

[MattAWard]

Hi I'm trying to register an MRI brain image to a CT scan but the result of elastix is the following nonsensical image:

Any idea what might be causing this? I start by linearly transforming one of the images onto the other which I use as the "Initial Transform", then run elastix with the default settings to produce this volume.

Thanks.

[lassoan]

Instead of setting initial transform, harden the transforms on the inputs. That would tell if the problem is with the initial transform setting or something else.