Dear Colm,
I've just got a look at your data. It seems that there
is definitely a scan that you should remove from the
study (the 13th, or volume 12 when looking at
GM_mod_merg in fslview). There are few others I am not
sure of. In those, the cortical grey matter ribbon
seems a bit thin (particularly for the first image)
but it could as well just reflect some effective
thinning.
In any case, I would consider doing a fslstats -V on
your *_GM_to_T images to get a feeling of how much of
an outlier some of them might be...
Hope this helps,
Gwenaelle
--- "Colm G. Connolly" <[log in to unmask]> a écrit
:
> Hi everybody,
>
> On 19 Sep 2007, at 15:51, Colm G. Connolly wrote:
>
> > In either case the data looks like the screen shot
> you attached to
> > your earlier email. Both the LPI and RPI look
> identical when
> > overlaid in fslview.
> >
> > I had originally thought that LPI would make fsl
> happier but since
> > RPI makes fslorient say "radiological" I'm going
> to try the RPI
> > files and see how things go. It'll be about 3 days
> before the job
> > completes.
>
> So I made the modifications to the data and re-ran
> my job and things
> seem, to my untrained eye, to be much better. Though
> since I've never
> seen this type of data before I'm not sure. I'd very
> much appreciate
> if someone more familiar with this type of analysis
> could have a look
> over the files and let me know what they think of
> them.
>
> I've been looking at the GM_mod_merge.nii.gz file
> and have notices a
> region of higher intensity which seems to migrate in
> a posterior to
> anterior direction as you go through the slices in
> the file. Is this
> a problem? What causes it?
>
> The file is at https://tcin.tchpc.tcd.ie/vbm/good
> along with the
> template_4D_GM.nii.gz.
>
> Thanks,
> --
> Dr Colm G. Connolly
> School of Psychology and Institute of Neuroscience
> The Lloyd Building
> University of Dublin
> Trinity College, Dublin 2, Éire
> Tel: +353-1-896-8475
> Fax: +353-1-671-3183
>
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