Dear SPM experts,

I am working with T1 images with a FOV where the edges of the skull (anteriorly and posteriorly) have been sliced off. Unfortunately this results in a misregistration in the frontal and occipital lobes during the segmentation process. I'm attaching pictures to help elucidate my problem.

Strategies eg using a skull-stripped T1 brain, switching to a larger TPM, changing the parameters of the bias regularization within the GUI, or running the segmentation process through Freesurfer, have not helped.

Does anyone know how to improve the T1 registration to the initial template?

Thank you,
yeeleng


T1 with "sliced" skull

Segmented GM overlaid on T1, showing misregistration

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