Hi,
Analyze format doesn't save enough information to really know if something
is correctly oriented in the left-right direction. What avworient will
tell you
is simply what FSL is defaulting to, but not necessarily what is
correct. You
need to check your conversion pipeline with some scans where you can
clearly
identify left and right - both in the structurals *and* in the
functionals to know
if this is working correctly. Even a phantom will do for this. Once
you know
that your conversion pipeline (MRIconvert in this case) is giving you images
that FSL and FSLView are correctly interpretting then you are fine.
However,
it doesn't sound like this is the case here. If you do this test and
things are
coming out left-right flipped, then you can rectify it using avwswapdim as
part of your conversion pipeline.
Note that comparing results on Analyze images with other software is
pointless
since everyone interprets Analyze slightly differently - because Analyze
does
not contain the right information. This is why the nifti format was
created, and
you can really only compare results between packages with any confidence
using nifti, which is what we'd generally recommend.
All the best,
Mark
Kate MacIver wrote:
>I have a data set of a right-handed task, using a standard protocol which
>gives activation maps which are bilateral, but predominantly ipsilateral M1
>and S1. I have used MRIconvert to convert the data to analyse format, but
>checked with avworient that the data is still radiological. I have used FSL
>3.2 for the full data set, but checked samples on FSL 3.3, still with
>strongly ipsilateral activation. I've checked the protocol with a healthy
>volunteer - on FSL we still have predominantly ipsilateral activation, which
>is contralateral when we use a different software package.
>Is there some point within FSL that the data could have been flipped? If so,
>is it possible to identify and rectify the problem?
>Kate MacIver
>
>
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