Dear Marina,
I don’t think mine was brilliant either. I think it might well be identical to yours. I have sent you an invite to a dropbox so you will be able to see for yourself.
But I thought it was an improvement on the result you initially showed. So I though it might be an avenue (i.e. manipulating the --refmask and the way the --refmask is or isn’t used in the different steps of the registration) for you to try. It would be a trial and error process though. And I think what might make the greatest difference might be to manually edit the --refmask so that it excludes those areas of high extracerebral intensity right next to the brain in the higher-up slices.
As I said, my preferred solution would be to build a new template that has this intensity. But this is not something I will be able to do short term.
Jesper
> On 16 Feb 2018, at 15:39, Marina Shpaner <[log in to unmask]> wrote:
>
> Hi Jesper,
>
> Sorry to pester you again. Do you think you could send me the registration you got to compare it to mine? Mine didn't really work that well.
>
> Thanks a million,
>
> -Marina
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