Hi Mark,
Thanks for the advise. The only thing that is flipped is
Anterior-Posterior. However, it seems that if I allow for a full search
for registration this does not cause a big problem.
Thanks,
Vina
Mark Jenkinson wrote:
> Hi,
>
> In Analyze you cannot store orientation information reliably (that's why
> we prefer nifti). FSL has historically adopted the same conventions for
> all Analyze images and these are the same as used in the avg152 images,
> which can be described as "radiological" but that sometimes has different
> interpretations by different people. See our FAQ for the precise
> definition.
>
> What I advise is to check the image by looking at it in FSLView, as this
> will show you the labels such as L, R, A, P, S, I. If these are
> correct then
> everything is fine. If the acquisition is not axial then these will
> be wrong
> but check the example_func2standard image and see if that is correct.
> If in doubt, run a test by doing something to the input image, inside
> the brain,
> such as manually editing some voxels to make them very dark which
> you can then use to mark left and right and see if that is propagated
> correctly.
>
> All the best,
> Mark
>
>
> Vina Goghari wrote:
>> Hello,
>> I'm working on a dataset collected a while back, where all the data
>> was stored as Analyze, but none of the orientation information was
>> stored in .hdr file. However, the data was stored in radiological
>> convention (right first then left). I was just wondering how FSL
>> handles this data with out info in the header and whether I have to
>> worry about the data being flipped. In the end the FSL post-stat maps
>> appear to also be in radiological convention.
>>
>> I hope this makes sense!
>>
>> Thanks,
>> Vina
>>
|