Hi Finn
See below.
On 26 May 2009, at 12:34, Finn Lennartsson wrote:
> Hi,
>
> Want to track projection fibers between PLIC and CP on one side, i.e.
> want to study the fiber trunk between these.
>
> Have defined PLIC and CP with two ROI:s, and want to use one of them
> as seed and the other as the end point. Ideally the end point ROI
> should be both be a waypoint and a termination mask. That is how I
> reason, or not correct? Does it work to define the same ROI to both
> being a wp and a term mask?
Yes, that is fine.
> My experience from termination masks (as also discussed on the mailing
> list before) is that the fiber extends some voxels beyond. For example
> using seeding in the PLIC ROI and using the CP ROI as a combined
> wp/term mask, the fibers still travels down below the pons and cross
> the mid-line with the middle cerebellar peduncle (MCP) and then travel
> up the CST on the opposite side.
This was a "feature" before the last patch. Shouldn't do that with
FSL4.1.3.
> To get rid of these fibers crossing in MCP I define an exclusion mask
> inferior to the CP ROI (fslmaths $subj/nodif_brain_mask -roi "all
> slices inferior to CP"). However then my fiber tract seems
> implausible, with missing fibers in the centre of the tract in a few
> slices superiorly of CP, as if CST fibers that has gone through the
> wp/term CP ROI then enters the termination mask and becomes excluded
> from the tract. Displacing the exclusion mask further inferiorly this
> does not occur, but then I can run into troubles with the MCP...
An exclusion mask is not what you want. It will exclude the whole of a
sample tract, even if you want to keep part of it...
> However, when I run it on FSL 4.1.3 then the missing fibers seem to
> appear. There is a release note:
> 4.1.3 23/04/09 Minor bug fix release
> ProbtrackX has a fix to termination mask usage
>
>
> What does this mean, that the problem with fibers traveling past the
> termination mask is fixed?
yes!
> Finally how should termination masks be used together with the other
> mask?
You can use them in conjunction with any other masks. The behaviour of
probtrackx should be the one expected from the respective role of each
mask.
>
>
>
> Cheers
> Finn
>
--
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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