I had the same error (skull strip failing on my EPI). In my case, I have partial volume EPIs (just a small slab in visual cortex). Adding Rick's suggestion worked for me.
Thanks!
Andrea
rick reynolds Wrote:
-------------------------------------------------------
> Hi Sarah,
>
> Maybe if we could see the data we could guess at
> what the problem is. On the other hand, try
> adding
> '-align_epi_strip_method 3dAutomask' to your
> afni_proc.py command, so that it does not use
> 3dSkullStrip for the EPI data, but uses
> 3dAutomask.
>
> Skull stripping is only to assist in the
> registration,
> and should not have any adverse affect.
> Actually,
> 3dAutomask seems pretty appropriate in general.
>
> - rick
