Hi Mark,
We have tracked down at least part of the problem. Nele was using SPM
normalized images which also had some nans, resulting in first_flirt
creating a matrix full of nans. I suggested that Nele try running with
the original images.
I will let Nele provide further input on what she finds.
Best,
Niels
On Fri, Nov 28, 2014 at 11:32 AM, Mark Jenkinson
<[log in to unmask]> wrote:
> Hi,
>
> Niels is right - I completely missed the -s option in your commands - my apologies.
>
> In this case it is quite unusual to see this kind of problem.
> Have you checked to see what the initial registration is like?
> If this is poor then it could cause this problem.
> The other situation that might be a problem is if there is a lot of atrophy in the accumbens and it cannot make the mesh thin/small enough. It would be useful to see the image in this case, so please upload an example to:
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>
> All the best,
> Mark
>
>
>
>> On 28 Nov 2014, at 09:06, Nele De Witte <[log in to unmask]> wrote:
>>
>> Hi Mark and Niels,
>>
>> Thank you for the response. I indeed already ask for the nucleus accumbens (and I also tried asking for the amygdala, but that also didn't work for these participants). Do you have any other ideas then, Mark?
>>
>> Niels, I will mail you the file of one participant. Thank you so much for your time!
>>
>> Sincere regards,
>> Nele
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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