Hi. If I understand you right, you want to look at the differences between
the "registered to the 3D" scans that is NOT due to atrophy....well, we
are defining atrophy to be "motion" at beain/non-brain edge points - so
are you looking for changes for example _within_ white matter areas? If so
I suggest that you adapt the SIENA script in the following way:
take the brain edge images (created by running siena_diff with the -d
option) and dilate them a couple of times with
"avwmaths <in> -dil -dil <out>"
then apply the relevant transforms from the registered to 3D images to get
them into the halfway space, apply the halfway brain masks, delete the
areas given by the above dilated edge mask, and subtract to find
differences.
Hope this is what you are after!
Thanks, Steve.
On Mon, 8 Jul 2002, Erik-Jan Vlieger wrote:
> Hi,
>
> I want to look at longitudinal change, possibly using siena. What I have is
> the following:
>
> At timepoint 1
> 1) A 3D T1W scan
> 2) Another scan, registered to the 3D
>
> At timepoint 2
> 1) A 3D T1W scan
> 2) Another scan, registered to the 3D
>
> I am interested in the difference between the scans registered to the 3D.
> However, I cannot directly compare these, as I expect that atrofy has
> occured. What I would like to do is to apply something like the inverse
> atrofie matrix, such that I can compare the registerd scans, look for
> differences, but discarding the differences that are a consequence of the
> atrofy.
>
> Is a scheme like this possible with siena and related tools?
>
> Thanks,
>
> Erik-Jan Vlieger
>
Stephen M. Smith
Head of Image Analysis, FMRIB
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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