Hi Arun,
The termination masks will stop the tracts that arrive at a mask, but
keep everything else. If you want to keep just the tracts arriving at
a given mask, you need to set it as a "waypoint" mask.
Cheers,
Saad.
On 25 Oct 2008, at 13:53, Arun Bokde, PhD wrote:
> Hi,
>
> I would like to map the tracts between two ROIs, and I have set up
> in the GUI the seed space with a single mask and the termination
> mask with another one. The results are such that all tracts
> starting from the first mask are detailed and the termination mask
> is not taken into account. The command statement in the window
> where I am running FSL shows the correct command with starting and
> terminations masks. I have switched the seed and terminations masks
> to see if that made a difference. The results were similar in the
> sense that the seed mask was used as the starting point for
> following all tracts without taking the termination mask into account.
>
> As a test, I used the same two masks as seed masks (using the
> multiple masks option). It worked correctly in that the tracts
> shown passed through the two masks.
>
> The options were the defaults settings. All masks are in the same
> space.
>
> The command shown in the terminal window when using a seed mask and
> termination mask is (I removed the full paths for brevity):
>
> probtrackx --mode=seedmask -x mask1.nii.gz -l -c 0.2 -S 2000 --
> steplength=0.5 -P 5000 --stop=mask3.nii.gz --forcedir --opd -s
> subj1013.bedpostX/merged -m subj1013.bedpostX/nodif_brain_mask --
> dir=subj1013_T4
>
> Any ideas as to what might be the problem?
>
> Cheers,
> Arun
>
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Saad Jbabdi,
Postdoctoral Research Assistant,
Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222545 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~saad
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