Thank you!
So there is no way to check before? - registration takes quite some time.
How do I decide if all_FA looks "ok"? What should I pay attention to?
Best,
Aga
On 26.07.2007 13:19 Uhr, "Steve Smith" <[log in to unmask]> wrote:
> Hi - in general small errors in the BET outline should not be a
> problem - I would run the full registration process and ascertain
> that the all_FA images look ok, in which case all is well.
> Cheers.
>
>
>
> On 26 Jul 2007, at 12:16, Agnieszka Burzynska wrote:
>
>> Dear all,
>> I am preparing my data for tbss and I believe having a good binary
>> mask is
>> crucial for good registration and other steps. After using default bet
>> setting from GUI I see that ofen the ventral part of medial prefrontal
>> cortex is cut off. If I manipulate with -g and -f from the command
>> line, I
>> et it better, but then too much of non-brain voxels are included
>> (like in
>> longitudinal fissure or on bottow of the brain).
>>
>> Is there any ´gold standard´for bet for dtifit/tbss?
>>
>> How the FA maps registration can be affected by too much non-brain
>> matter?
>>
>> Is it recommended to first center my images and use avwroi to cut
>> the sides
>> of the image to improve the bet results? Or as long as the mask is
>> ´roughly
>> ok´I can be happy with the outcome?
>>
>> Thank you,
>> Aga
>
>
> ------------------------------------------------------------------------
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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