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
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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
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