Hi - i understand what's happening here _partly_ : there is a bug in the
old version of fslview which means that Talairach coords get reported with
a slight offset compared with the true values (eg what get reported in the
FEAT tables). This is fixed in the new version.
However, if bg_image and avg152T1 have the same header info then I would
expect any repoting from fslview to be identical - is it not?
Cheers.
On Thu, 8 Jul 2004, Jonas Kaplan wrote:
> Just a follow-up on this...
>
> In a group analysis, the bg_image created seems to have different
> coordinates from the
> avg152T1 atlas which it was registered to. That is, when functional
> data is overlaid on the
> bg_image the peaks come out off by 2 mm in the X direction, 4 in the y
> direction, and 2 in the
> Z direction relative to what is reported in the cluster list. However,
> when the functional data
> is overlayed on the avg152 atlas, the coordinates from the list match
> where the peaks are. Why
> would the bg_image have different coordinates if everything is
> registered to the standard
> space during a group analysis?
>
> Thanks,
>
> Jonas
>
>
> On Jun 25, 2004, at 7:33 AM, Stephen Smith wrote:
>
> > Hi - they should correspond in general - if you look at a first-level
> > analysis and look at the non-Talairach-space version of the cluster
> > table,
> > the voxel positions should correspond to the voxel positions shown in
> > FSLView. Does this work for you? The only minor issue might be that
> > FSLView is about half a voxel out when showing standard-space images
> > and
> > reporting mm co-ordinates - that'll get fixed in the next version.
> >
> > Cheers, Steve.
> >
> >
> >
> > On Fri, 18 Jun 2004, lucina wrote:
> >
> >> Hi, I have a question about FSL view: In trying to locate the peak
> >> voxels, I used the local maxima table that you can find in the
> >> report.html for each contrast. However, it seems that the coordinates
> >> listed there don't match up with the actual peaks I can see in FSL
> >> view. In other words, the coordinates listed in the tables don't
> >> correspond to the peak activations in FSL view. Any ideas? Thanks,
> >>
> >> Lucina
> >>
> >> --
> >> Lucina Q. Uddin
> >> UCLA Psychology-Cognitive Neuroscience
> >> Box 951563, B627 Franz Hall
> >> Los Angeles, CA 90095-1563
> >>
> >
> > Stephen M. Smith DPhil
> > Associate Director, FMRIB and Analysis Research Coordinator
> >
> > Oxford University Centre for Functional MRI of the Brain
> > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> > +44 (0) 1865 222726 (fax 222717)
> >
> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >
> >
>
> --
>
> Jonas Kaplan , Ph.D.
> Ahmanson-Lovelace Brain Mapping Center
> University of California, Los Angeles
> Los Angeles, CA 90095-1553
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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