Hi Mark,
Yes part of the bottom of the brain is not covered (3.125 voxel & 26
slices, 1.5 TR). I also used a full brain search, if that helps. Just
wondering if it is inappropriate to use non-linear in this case?
Thanks,
Vina
Mark Jenkinson wrote:
> 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
>>> ---------------------------------------------------------------------------
>>>
>>
|