P.S., To visualize the problem: The seed is the pallidum, and in this attached screenshot, you can see in the sagittal view traces going up into the cortex. Blue shows the termination/waypoint mask (M). I had hoped to see only tracts running in the subcortical region. 

Would one way to clean this up be to limit the number of steps? From past posts, it looks like maybe these paths go out of the subcortical region and then back to the mask which is why they've survived?

Thanks for your help,

Jake

<Screen Shot 2013-04-03 at 4.14.11 PM.png>

On Apr 3, 2013, at 3:22 PM, Jake wrote:

Dear FSL list,

I did some searches on the board and found some similar posts but am still confused as to why my tractography results look the way they do.

Basically, I am using a single seed ROI (S) and made a single mask with multiple ROIS in it (M).  I set (S) as the single seed mask, and (M) as a waypoint. I also set (M) as a termination mask. However, after running probtrackx, when I open fdt_paths, the tracing goes past the areas in (M) and to the rest of the brain. It look like the termination and waypoint functions didn't work. How could I fix this?

Thanks for your help in advance,
Jake

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