Hi Steve,
I read this note with some concern, given that a couple of my colleagues are
using TBSS to evaluate hemispheric FA asymmetries. In looking over their
results, I think they have found too many significant voxels (including a
large number of the highest possible significance). What biases one might
expect if they used the publically released TBSS scripts to perform a
hemispheric FA asymmetry study?
Thanks,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Steve Smith
Sent: Thursday, May 14, 2009 11:23 AM
To: [log in to unmask]
Subject: Re: [FSL] Symmetrical TBSS skeleton
Hi,
Yes - when you want "tbss_skeleton" to use a specific skeleton rather
than one derived from the 4D data you feed in, you need to use the -s
flag (see the usage).
Also, you need to explicitly force the skeleton to be symmetric and
not just derive it from a symmetric mean FA image (the skeletonisation
will not necessarily give an _exactly_ symmetric skeleton when fed a
symmetric image).
We have a script for doing asymmetry analyses which we will clean up
and make available soon - hopefully next week.
Cheers.
> Hi,
>
> Just to correct my last post - what I get at the end of this
> processing
> pipeline is an 4d all_FA_skeleton file that IS symmetrical but does
> not
> quite fit my original "symmetrised" mean_FA_skeleton in that there are
> additional/missing voxels in places.
>
> Is this a reasonable method to achieve what I am after, or is there an
> alternative method.
>
> Thanks.
>
> Pete
>
On 11 May 2009, at 12:44, Pete Goodman wrote:
> Dear All,
>
> I am trying to use TBSS to derive asymmetry indices. To do this I
> have,
>
> 1) Made the FA template symmetrical by creating a flipped version
> (fslswapdim applied) and averaging the flipped and unflipped versions
> 2) Registered all data to new template using tbss scripts 1, 2 and 3
> 3) Taken the mean FA skeleton and made this symmetrical using the same
> method as above
> 4) Fed my all_FA data into tbss 4 together with the new symmetrical
> skeleton
> - here I was expecting voxels from each subject to be projected onto
> the
> symmetrical skeleton which I could then flip again and use
> (unflipped minus
> flipped) to derive AI.
>
> However, the all_FA_skeletonised output I get is not quite
> symmetrical. The
> deprojection step seems to have ignored the use of the new symmetrical
> skeleton, and instead used the old, unsymmetrical one.
>
> Any help, tips as to a better method would be welcome.
>
> Thanks.
>
> Pete
>
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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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