Hi Colm,
looking at your image, I think it's fine.
There must be some hypointensities in the white matter of your patients that explains the resuts in the white matter.
The results in the ventricles is quite likely the consequence of two things: first the interface ventricle/white matter can be sometimes identified as grey matter by the automated tissue segmentation and second, there might be some slight residual misalignment of the ventricles (presumably quite big in your patients?) which leads to this result. Looking at your native GM images in the patients would give you a clue about this.
There are still some significant and very well defined results in the precentral gyrus bilaterally for instance...
Hope this helps,
Gwenaelle
--- En date de : Lun 19.10.09, Colm Connolly <[log in to unmask]> a écrit :
> De: Colm Connolly <[log in to unmask]>
> Objet: [FSL] fsl vbm differences in white matter around ventricles
> À: [log in to unmask]
> Date: Lundi 19 Octobre 2009, 14h18
> Hi everybody,
>
> I've been running a VBM study with 2 groups (c and u) of 43
> people each. The randomise run is a simple t-test with an
> added covariate (age) because the groups are not exactly
> matched on this variable.
>
> The first contrast (c > u) (to my eye) looks ok, the
> differences are in regions that are clearly GM. The opposite
> contrast (u > c), on the other hand, has me concerned.
> There are many regions that survive thresholding of the
> tfce_corrp_tstat2 at 0.95, but many of these regions are
> around ventricles and in white matter. Has anyone seen
> something like this before? The offending tstat image is
> available at https://tcin.tchpc.tcd.ie/~colmconn/cVsUWithAge_tfce_corrp_tstat2.nii.gz
> I necessary I can make other files available if it will help
> diagnose the problem (assuming that it is a problem). The
> subjects are listed in the GM_mod_merg file in the order c
> followed by u.
>
> Any help most gratefully accepted.
>
> Regards,
> --
> Dr Colm G. Connolly
> Institute of Neuroscience
> The Lloyd Building
> University of Dublin
> Trinity College, Dublin 2, Éire
> Fax: +353-1-671-3183
>
> Please note that electronic mail to, from or within the
> Trinity College Dublin, may be the
> subject of a request under the Freedom of Information Act.
>
>
>
>
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