Hi,
Are you using a partial field of view?
Is the cut-off due to it being at the bottom of the image in either the
input or reference image?
All the best,
Mark
On 12 Nov 2008, at 13:54, Vina Goghari wrote:
> Thanks that explains part of it. With the linear transformation
> there is part of the temporal cut-off (which appears to be
> appropriate). With the non-linear it appears the brain is stretched,
> there appear to be parts of the temporal lobe present that was not
> present before.
>
> Thanks,
> Vina
>
> Steve Smith wrote:
>> Hi - we definitely see improved registrations (of the structurals
>> to standard space) when adding FNIRT on top of the affine FLIRT-
>> derived transformation. One possibly confusing factor is the end-
>> slice interpolation is currently different when using FNIRT
>> (that'll be made more consistent in future) so it may appear that
>> the very top and bottom of the data are 'stretched' (though this
>> shouldn't affect any higher-level analyses as it should be outside
>> the standard space brain space). [Jesper - did I get that bit
>> right?]
>>
>> Cheers.
>>
>>
>>
>> On 12 Nov 2008, at 01:53, Vina Goghari wrote:
>>
>>> Hi,
>>> I used the older FSL version previously with FLIRT to register my
>>> images. With this new version I also used the nonlinear Warp
>>> Resolution as well with default of 10 (same subject). The other
>>> search options remained the same. However, it appears the
>>> registration does not look as good with the new version in some
>>> regards? I wasn't able to attach images...
>>>
>>> Thanks for any insight you can provide!
>>>
>>> Vina
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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