Hi,
There is certainly no random or unset internal variable with FLIRT.
I have never seen this behaviour and am puzzled by it.
Are you using the most recent version of FSL (4.1.6)?
And if you run fslorient on the images that go into creating
the template, are they all of a consistent orientation, or are
they mixed?
I'm glad that -usesqform works though.
All the best,
Mark
On 14 Dec 2010, at 20:06, Robert Devins wrote:
> 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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