Hi
Try doing the same tracking but without waypoint, and see if (1) the fdt_paths file looks like it's picking up sensible white matter tracts, and (2) if these reach the superiortemporal mask.
Saad.
On 12 Nov 2010, at 19:44, Shugao Xia wrote:
> Thanks. I used mri_annotation2label to create the labels and use lh.lateralorbitofrontal.label and
> lh.superiortemporal.label to track the uncinate fasciculus.
>
> I converted lh.superiortemporal.label to lh.superiortemporal.nii.gz using mri_label2vol
> I used probtract as
> probtrackx -x lh.lateralorbitofrontal.label --mesh=lh.white.asc --xfm=fs2fa_warp --invxfm=fa2fs_warp --seedref=brain.ni.gz -s ../merged -m=../nodif_brain_mask --dir=fibretrack -l -c 0.2 -S 2000--steplength=0.5 -P 5000 --forcedir --opd --waypoints=lh.superiortemporal.nii.gz --stop=non_wm_mask.nii.gz
>
> But I got empty tract. I think that I got empty result since of --waypoints option. lh.superiortemporal is a ROI in the coritical region, it is supposed that there is no tract passing this ROI. My understanding is that Probtractx doesn't use an FA threshold and use consistent directions to follow for tractography. Generally, the fibre tracks will turn away from the cortical regions when they are in the vovels near the cortical regions. So the target mask can not be in the cortical regions. But I think that my understanding is wrong, since I knew there were success using the target mask in the cortical regions from old archive. Could you please help me clarify?
>
> For my case, what should I do on your experience?
> Thank you very much
>
> Best
>
> Shugao
>
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