Hi Josh
Streamlines can sometimes cross to the other hemisphere outside of the commissures due to the combination of high anisotropy in the cortex and occasional proximity of the cortices from both hemispheres. You can use a planar exclusion mask that separates the two hemispheres if you want to avoid this completely.
Cheers
Saad
> On 10 May 2019, at 14:21, Josh Robinson <[log in to unmask]> wrote:
>
> Hi all,
>
> I am trying to track between striatal subregions and frontal regions unilaterally. I have set a text file containing a mask of the corpus callosum and the other striatal subregions of non-interest as my --avoid parameter in my command. My resulting paths distribution has indeed blocked off the corpus callosum, however I still have a very large number of fibers crossing hemispheres, some look as though they are jumping the longitudinal fissure.
>
> I'm guessing this is more of an issue with the quality of my data, but is there any other explanation out there as to why this may be happening?
>
> Here's the command I ran:
>
> probtrackx2 -s bedpostX/merged -m bedpostX/nodif_brain_mask.nii.gz -x left_limbic_striatum.nii.gz -o left_limbic2OFC_restricted --targetmasks=left_OFC_bin.nii.gz --dir=restricted_tracking --opd --pd --s2tastext --avoid=avoid.txt --wtstop=left_OFC_bin.nii.gz --nsteps=1000 -l --modeuler -V 2
>
> Thank you for your help,
>
>
> Josh
>
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