Hi - it is hard to tell what's going on from the picture that you sent. Do you actually get the IFO tract?
Also, the frontal lobe has massive connections to the thalamus, and tractography has no reason to stop there. So maybe what you are seeing are connections between the thalamus and the frontal lobe combined with connections from the thalamus to the occipital lobe. You may want to edit your seed mask and put an exclusion mask in the thalamus.
Cheers
Saad
On 7 Nov 2012, at 19:41, Slagle, Anna (NIH/NIMH) [F] wrote:
> Hello all,
>
> I am using probtrackx2 to trace the inferior fronto-occipital fasciculus with distance correction. I am using a seed mask in the frontal lobe (green in attached image), termination mask in occipital (blue in attached image; also serves as a waypoint), waypoint mask in the external capsule (not visible in this slice), and exclusion masks anterior to the seed, posterior to termination, and interhemisphere (not pictured). As shown in the attached image, I am getting fibers tracking in the cingulum and through the thalamus, neither of which should be possible given the location of my waypoint mask. The fibers in the cingulum can be thresholded out with a low threshold value, but those through the thalamus would require a very high threshold to get rid of these fibers.
>
> Any possible explanations as to why these fibers are there and how I can prevent them? Thank you in advance for your help.
> Command line code used to run this is below.
>
> probtrackx2 -x frontal_seed_roimask.nii.gz -V 1 -l --onewaycondition --wayorder --pd -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --avoid=./exclusions.txt --stop=occipital_termination_roimask.nii.gz --forcedir --opd -s bedpostX/merged -m bedpostX/nodif_brain_mask --dir=./IFO_tract --waypoints=./waypoints.txt --waycond=AND
>
> Best,
> Anna
>
>
> ----
> Anna Slagle
> Post-Baccaulaureate IRTA
> Unit on Multimodal Imaging Genetics (UMIG) CBDB—GCAP—NIMH—NIH
> 10 Center Dr,
> Rm. 3C205
> Bethesda, MD 20892
> Phone: (301) 435-4599
> <strange_cingulum.jpg>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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