Hi,
The two things aren't 'comparable' in that sense. TBSS aims to find
the centres of common (across subjects) tracts, whilst the Oxford
thalamus atlas segments (in a probabilistic way) the thalamus
according to where its different regions primarily connect to on the
cortex - so there's no direct representation of any tracts in the atlas.
Steve.
On 26 Jul 2009, at 11:53, Hedok Lee wrote:
> Dear Steve,
>
> Thanks for your response, and my apology for not being very clear.
> Basically, I found results in thalamus and am wondering whether I
> should interpret the results as though skeltonized tracts are
> associated with "Oxford thalamic connectivity atlas." When I
> compared default skletonized atlas provided by FSL with the
> connectivity atlas, skletonized tracts do not appear to resemble the
> connectivity atlas.
>
> Question: Can I interpret TBSS results in thalamus and relate that
> with connectivity atlas?
>
>
> Thanks in advance,
>
> Hedok
>
> Steve Smith wrote:
>> Hi,
>>
>> You are correct in saying that the search direction
>> ('perpendicular' to the local skeleton) is determined purely by the
>> local gradient (and second derivative) of the FA, and not taking
>> into account tensor eigenvalues. There are many other sources of
>> information that can potentially aid the registration, including
>> the eigenvectors, but we've concentrated on what seems to matter
>> the most.
>>
>> I wasn't sure what your actual question was?
>>
>> Cheers.
>>
>>
>> On 24 Jul 2009, at 19:52, Hedok Lee wrote:
>>
>>> Dear FSLers,
>>>
>>>
>>> I have a general question about projecting skeltonized FA onto a
>>> template.
>>>
>>> From what I understand projection of the skeltonized FA is
>>> performed by
>>> displacing skeltonized voxels to match a template skleton. This
>>> step is done
>>> by using a position of voxel and its FA, but it does not take into
>>> account
>>> for the direction of principal eigen vector in the voxel. In other
>>> word,
>>> when principal eigenvector is weighted with FA map, we can color-
>>> code a
>>> voxel with FA and its orientation (Red, Green, and Blue), so the
>>> projection
>>> should be done by matching not only FA but with its orientation as
>>> well
>>> (being homologous may be the right term ?).
>>>
>>> I think this also applies to skeltonizing step too.
>>>
>>> Perhaps, I’m missing something here. Let me know if anybody has
>>> any opinion
>>> on this.
>>>
>>> Thanks,
>>>
>>> Hedok
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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