Hi - if you can't see the optic tract by placing a seed in the tract
and visualising the output, then there is something wrong with your
data.
The first thing to do is just to use single seedmask mode to see if
you can visualise the tracts. If you can't see anything in this mode,
you need to go back to your data.
The most likely problem is your bvectors being wrong. You should
check dti_v1 in lines mode. The lines should make continuous
pathways in all 3 planes.
If they do, you should check whether your data is neurologically
oriented (fslorient -getorient)- if this is the case there are a few
problems to overcome but it is do-able. We can walk you through it.
If everything looks good and your data is radiological but you still
can't see the major pathways, you can stick the data on out upload
and someone will take a look over the next few days
www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
Cheers
T
On 24 Feb 2008, at 01:04, Anastasia Ford wrote:
> Matt and FSL experts,
>
> I will try to run the probtrackx from the command line using your
> suggestion.
> I also tried mapping the optic tract by using a single mask of the
> optic
> chiasm and the resulting tracks do not look correct. None of them even
> reach the occipital cortex, and very few reach LGN. Are thre any
> general
> guidelines for tract mapping in terms of mask seeds? For example,
> should I
> always try to use the symmetric approach you mentioned, or use one
> mask
> that would contain say the chiasm, LGN, and the visual cortex?
> Im really struggling with what options to choose and very few of my
> tracks
> come out correct. I would appreciate if someone could walk me
> trough the
> mapping process of one prominent tract (how many masks, wapoints,
> exclusion masks).
>
> I appreciate your help,
>
> Anastasia
>
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