Hello TrackVis!

I have a question regarding treating voxels with a value of 0 as NaN.  I currently have some tracts separated in 34 different subjects.  I extracted FA values from voxels that the fibers pass through for a group analysis. 

My question is: Is there anyway to threshold the Image you load in so not to include voxels with FA <0.3?  I can create the thresholded FA image for each subject using FSL but TrackVis still includes voxels with value 0 in the analysis, greatly skewing the mean FA downwards.

Any help would be much appreciated!

Thanks,

Daniel

Hello, 

Thanks for the response.

By this do you mean change the Mask threshold before creating the .trk file in DTK?

I'm trying to find some sort of track threshold option within TrackVis and can't seem to find it.  

Many thanks,

Daniel

Hello again,

I attempted to make the mask threshold min:30 max:100 (unchecked auto) as the values in the DWI are from 0-100 not 0-1.  However when I check my existing track's statistics within TrackVis it is still including voxels under 0.3 FA, as shown in the histogram.  I am probably doing something wrong but I'm unsure of how to proceed.

Is it only possible to do this thresholding in the commandline? I have been using the GUI and none of the DTK commands (e.g. dti_tracker) seems to be working.. probably need to set something up for that on my end.

Thanks again for all your assistance!

Daniel