Hi Gwenaelle,
Thanks for replying.
On 21 Oct 2009, at 14:52, Gwenaëlle DOUAUD wrote:
> 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.
I have noticed that some of the MPRAGE images are noisy and that the
segmented images reflect this: some white is classified as grey. My
understanding is that FAST should be able to deal with some noise in
the data but maybe there is more noise than the default parameters in
the fsl scripts can handle. Is there a way to tune it to make it more
robust in the face of noise in the T1s?
Take for example this person:
https://tcin.tchpc.tcd.ie/~colmconn/short.66128.anat_struc.nii.gz and
the corresponding GM map https://tcin.tchpc.tcd.ie/~colmconn/short.66128.anat_struc_GM.nii.gz
some of the white matter is classified as GM. Do you think is there a
way of dealing with this?
( https://tcin.tchpc.tcd.ie/~colmconn/GM_mod_merg_s2.nii.gz is also
available. Volumes 80-83 (among others) show regions which to my mind
should be WM )
One more thing, with respect to residual misalignment, I have run the
vbm as follows:
fslvbm_1_bet -N -B -f 0.3
fslvbm_2_template -a
fslvbm_3_proc
might it be advisable to run the analysis with fslvbm_2_template -n?
Might the nonlinear tuning mitigate misalignment assuming it's there?
> There are still some significant and very well defined results in
> the precentral gyrus bilaterally for instance...
>
Sure, but there remains the problem of trying to explain the large
blobs located around the ventricles, it could be problematic to get by
reviewers, otherwise there are some really neat results in the dataset.
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.
|