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Hi Saad,

I re-ran tractography using the following command:

probtrackx2  -x ${seed_dir}/${roi}_native.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --stop=${seed_dir}/termination_mask_native.nii.gz --forcedir --opd -s merged -m nodif_brain_mask --dir=${roi}_mult --waypoints=${seed_dir}/termination_mask_native.nii.gz --waycond=AND

And it is still giving me results past my expected area similar to the screenshot I sent before. If I threshold fdt_paths to ~20, most of these outside results go away. Do you think my termination mask is failing, or that these are signals that are going cortically and then back to the subcortical regions, which is why they survive?  I'm now using FSL 5.0.2.  Thank you again for your time and help,

Sincerely,

-Jake


On Apr 4, 2013, at 11:44 AM, Saad Jbabdi wrote:

Hi - if you're using the latest version (FSL5.x) then the GUI should be running probtrackx2 with the --onewaycondition flag turned on by default.
Yes this flag is specific to probtrackx2. The flag doesn't exist in probtrackx, and the default there is as if the flag was not set.

Cheers
Saad



On 4 Apr 2013, at 16:23, John Kuster wrote:

Hi Saad!

I'm running probtrackx from the GUI… and I noticed it doesn't seem to be using the --onewaycondition flag. I didn't see an option in the GUI to use that when I looked just now too, is this specific to probtrackx2 only? If so I will work on being able to use probtrackx2.

Thanks for your help!!

Jake


On Apr 4, 2013, at 4:12 AM, Saad Jbabdi wrote:

probtrackx2


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