Hi,
Just to add to this - please don't use fslswapdim directly, as it is easy to do the wrong thing with it.
Use fslreorient2std instead as it is much easier and specifically designed for this use.
All the best,
Mark
On 8 Jul 2011, at 08:12, Stephen Smith wrote:
> Hi - this almost certainly means that the registration to standard space didn't work in the first place - have you checked that?
>
> You might want to pre-flip the datasets using fslswapdim so they are in the same orientation as the MNI152 standard space before running SIENAX - that might help with your sagittal scans.
>
> Cheers.
>
>
>
> On 7 Jul 2011, at 17:32, lukasz priba wrote:
>
>> Dear FSL experts,
>>
>> I've been having some probrems with getting my mask from standard space (registered with MNI brain template) to a native space of some images in my sample. I'm using I_std_inv.mat matrix file (one of sienax outputs) to get my mask into native space-it works perfectly fine for 51/60 images. Oddly all 9 images that fail are sagital images(although it works fine for 11 other sagitals).
>> I find it quite bizzarre that the transformation doesn't work properly, even though the segmentation works perfectly fine. Is there something wrong with the transformation matrix or has it something to do with the orientation of my images?
>>
>> Lukasz
>>
>
>
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> Associate Director, Oxford University FMRIB Centre
>
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