I found out that by adding -usesqform to the FLIRT steps this problem
goes away. One thing I wonder: the randomness of the flipping (when
-usesqform is not used). Is it possible there is an un-initialized
variable inside of FLIRT so that it picks one orientation vs another, at
random, depending on the initial state of memory? Just wondering.
In any case, this seems to be solved - thanks for the suggestion.
Stephen Smith wrote:
> Hi - the first thing to tie down is whether the problem is in the
> FLIRT registration, or a header problem.
> Cheers.
>
>
> On 10 Dec 2010, at 19:59, Robert Devins wrote:
>
>> Hi,
>>
>> I've been trying to run fslvbm, and find that some if the images in
>> the 4D template (after the fslvbm_2_template) step are exactly
>> flipped about the X-axis. The brain images going into that step are
>> not flipped, and look good. Which ones are flipped seem to be kind of
>> random, and often not repeatable. I've tried adding the -noshape
>> option to the flirt steps, but that doesn't fix the flipping issue
>> and makes the warping even worse (again randomly on some images).
>> Does anybody have any thoughts or have seen this?
>>
>> Thanks - Bob Devins
>>
>
>
> ---------------------------------------------------------------------------
> 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] <mailto:[log in to unmask]>
> http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/%7Esteve>
> ---------------------------------------------------------------------------
>
>
>
--
Bob Devins
Vermont Advanced Computing Center
Clinical Neuroscience Research Unit
University of Vermont, Burlington VT
(802)656-0141
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