Hi, we are also having this problem after using bet. I am attaching a
document with the details for our system that you asked Matt for, in
the hope that this can help you track down the problem, thanks,
Jeff
On 5/15/06, Mark Jenkinson <[log in to unmask]> wrote:
> 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
>
|