Dear Matt,
I cannot replicate this problem at our end with any combination
of Analyze or Nifti.
Could you please let me know the following details:
- your platform
- the version of FSL you are using
- the avwhd output of the input and output images
- the exact commands that you are running
Hopefully this will let us track it down.
All the best,
Mark
On 15 May 2006, at 19:31, Matt Holloway wrote:
> Hi,
>
> I'm trying to brain extract and noise-reduce a set of T1 structural
> images
> to get these images ready for VBM analysis in SPM2. While the
> process of
> Brain extracting and SUSAN are going smoothly, and nicely brain-
> extracted
> and de-noised images are being produced, I can't figure where the
> coordinate
> system is getting modified. Immediately following Brain-Extraction
> the "mm"
> values in FSLview on the X, Y, and Z planes are changing from the
> original
> ~-90mm to +90mm on say the X-axis, to something like 21090mm to
> 21170mm.
>
> I believe this modification of the raw-coordinates may be playing
> into so
> difficulties making a custom t1-template from these images down the
> road.
> I'm also seeing some changes in the header files evident by using
> avwinfo,
> in terms of the size of each dimension.
>
> Any insight you could offer would be wonderful.
>
> Thank you
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