on filtering tractography with inclusion and exclusion ROIs

[s guo]

Hi,

I am currently working on filtering a brain tractography using TractTool. Instructions in "Second Step: Defining each tract" on http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.TsaAdvanced say to first filter with an inclusion_ROI.nii.gz  and then filter to exclude the exclusion_ROI.nii.gz. 

My situation is that an entire shaded area included in my exclusion_ROI.nii.gz has appeared in my output.nii.gz.

I used the following commands as per the guide above:

TractTool -in tensor.vtk -filter filtered_tract1.vtk -roi ROI_inclusion1.nii.gz

TractTool -in filtered_tract1.vtk -filter filtered_tract2.vtk -roi ROI_excluded1.nii.gz -inclusion 0

TractTool -in filtered_tract2.vtk -nifti output.nii/.gz -target mean_diffeomorphic_initial6.nii.gz

One question I have is about the inclusion and exclusion ROI inputs. In the guide, it looks like these are just 1 dimensional lines. How does the program interpret this? Is there a reason why different labels were used for creation of the corpus callosum?