Dear all experts,
I want to see the streamlines connecting two regions.
So after generating global tractography using
tckgen , I used
tck2connectome to get the connectome matrix of some ROIs. Then I used
connectome2tck to extract the streamlines between any two nodes of those ROIs.
However,it seems likely that there are some wrong assignments of streamlines. What it means that when I open the track between nodes1 and nodes2 using mrview GUI, for example, “streamlineofnodes1-2.tck” , there are some streamlines assigned in nodes3. In fact, the nodes3 is rather far away from nodes1 and nodes2.
I don’t know if there are wrong during I processed.
Here are the commands I used:
tckgen -algorithm Tensor_Prob -select 200000 -angle 20 -cutoff 0.1 -seed_image b0_mask.mif -fslgrad bvecs bvals DWI_200K.tck
tck2connectome DWI_200K.tck ROIs_labelconvert.mif tensor_200K_connectome.csv -assignment_radial_search 0.4 -out_assignments streamlineofnodes
connectome2tck DWI_200K.tck streamlineofnodes streamlineofnodes_out -files per_edge
By the way, the datas I analyzed were rat brain, the voulme is 0.001 times of human brain. So the assignment_radial_search I chose was 0.4
Thanks very much for your patience.