Hi - yes, I'm afraid you're right - you really need FreeSurfer to get
these things done right!
Cheers.
On 7 Aug 2009, at 10:35, Simon Rushton wrote:
> I have been doing my analysis using Feat and then displaying results
> on inflated brains (generated using Freesurfer). I've run into what
> I presume are very old problems -
>
> First, because Feat smoothing is based on voxels in a 3d volume,
> activation is spread across abutting grey matter edges. This leads
> to the problem of trying to separate true and "ghost'' activation
> when the results are displayed on a surface (I appreciate I can
> potentially disambiguate the two by doing a separate run with no
> smoothing but then that would require me to tamper with the smoothed
> images to remove the "ghost" activation, something I'd rather not do).
>
> Second, I'm interested in activation in some fairly small anatomical
> areas (take MT+, the motion complex, as an example) and the location
> of these areas vary relative to the rest of the brain. So when I do
> a group analysis the same anatomical areas are not superimposed very
> well and hence I don't find the activation I expect from inspection
> of the individual analyses.
>
> Now, one way round these two problems would be to switch from FSL to
> Freesurfer for analysis. Freesurfer will do surface based smoothing
> which should remove the ghosting problem. It also allows surface
> maps of individual brains to be morphed to superimpose anatomical
> locations in a group analysis. However, it would be a lot of effort
> to learn Freesurfer and redo all my analyses, so, before doing that:
>
> 1. Are there some FSL solutions to these problems? For example, at
> least in my head, it seems like it should be reasonably easy to do
> some "smart" volume based smoothing that does not include voxels
> that are separated by something other than grey matter. Has anyone
> written a simple plugin "smart smoother" for Feat? Also, the new
> non-linear registration might be expected to solve some of the
> registration problems , maybe I just need to plug in the right
> parameters? In which case, what are they?
>
> 2. If I need to go the Freesurfer route, does anyone have any
> guidance re how to do this as easily, preferably sticking with Feat
> as much as possible? I did find this
>
> http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
>
> but the section on doing group based surface analyses first notes
> "FSL tools have not been extensively tested on surface-based data"
> which seems to be pushing me away from Feat, and then after a rather
> terse set of Freesurfer instructions suggests consulting the
> Freesurfer wiki. I interpret this as "now go and learn Freesurfer"!
>
> Any guidance would be much appreciated...
>
> simon
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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