Hello,

I am trying to extract tracks between two rois and trying to save the output track as a volume in nifti format unsuccessfully. Can you please help me with the commands?

This is what I am doing right now:

track_vis /path/streamline_final.trk –roi /path/region3.nii –roi2 /path/region35.nii –output_volume path/testtrk.nii

When I use the above command (all together) I get zero tracks in the output volume. (I have already extracted a big track for these ROIs using the GUI).

- Do you use the three commands separately or together in one command as above? Do you have to upload the trk file for every command if you are using them separately? 

- Do you close the visualization toolkit before typing the next command?

Thank you for all your help,

CB