Hi - yes, when running on "olles" (the ROI'd data) the results are
actually quite reasonable (there are often some slight errors in the
BETting or segmentation, particularly when the slices are fairly thick) -
the results improve a little if you use -f 0.4 or -f 0.45.
Cheers, Steve.
On Tue, 6 Dec 2005, Lisa Botes wrote:
> Hi.
>
> I have some coronally taken images. I have stacked them in MRIcro and then
> swapped them with avwswapdim, to correctly place them in space, in
> accordance to the standard brain in fsl.
>
> I have run sienax on the "original" images and also on the same set where I
> have used avwroi to cut away the first 81 slices (since there are a lot of
> neck and throat in the images).
>
> The first sienax run includes a lot of soft tissue of the throat. Soft
> throat tissue is not included in the segmentation of the "cut" image.
> However, here the segmentation has excluded a lot of brain tissue at the
> frontal pole and at the top of the brain.....
>
> Why does sienax exclude certain braintissue in the "cut" image and not in
> the "original" one? Isn't the COG "optimized" in the "cut" image?
>
> I have tried improving the segmentation with the -f and -g option as well
> but it didn't work well.
>
>
> The resulting images can be found at
>
> www.smile.ki.se/uploaded_files/tarfile.tar
>
>
> Thank you for an excellent webpage!
>
> Best regards,
> Lisa Botes
> Hospital Physics,
> Huddinge University hospital
>
>
>
>
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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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