First of all, I am sorry for the lengthy question and I am a newbie Tractography analysis. In addition, I have read previous posts about generating streamlines from ROI to ROI. The purpose of my analysis is to perform a seed-based tractography from source ROI to other regions of shen atlas, I have tried two different methods but I am not sure if they are corrected.
1>Create a binarized source mask from co-registered atlas(atlas.nii.gz)
2>tckgen FOD.mif tracked.tck -act 5TT.mif -seed_image source_roi.nii.gz -seeds 0 -select 5000000 - seed_unidirectional
3>tcksift2 tracked.tck FOD.mif prob_weights.txt
4>tck2connectome tracked.tck atlas.nii.gz conmat.csv -vector -scale_invlength -tck_weights_in prob_weights.txt -assignment_radial_search 2 -scale_invnodevol. By completed all these steps, would it generate a 1-D connectivity matrix that contain structural connectivity from seed region to the rest of regions in the atlas.
1>whole-brain tractography tckgen FOD.mif tracked.tck -act 5TT.mif -seed_gmwmi gmwmi.mif -select 5000000
2>tcksift2 tracked.tck FOD.mif prob_weights.txt
3>tck2connectome tracked.tck atlas.nii.gz connmat.csv -zero_diagonal -symmetric -assignment_out assignment_atlas.csv -scale_invlength -tck_weights_in prob_weights.txt -assignment_radial_search 2 -scale_invnodevol
4> **connectome2tck -nodes 146 tracked.tck assignment_atlas.csv -files per_node source_146_tracked.tck -tck_weights_in prob_weight.txt -prefix_tck_weights_out source_tracked_weights.txt. This would give me all streamlines emerge from source ROI to the rest of atlas region.
5>**tck2connectome source_146_tracked.tck atlas.nii.gz connmat.csv -scale_invlength -tck_weights_in source_tracked_weights.txt -assignment_radial_search 2 -scale_invnodevol -vector. Is this last step plausible since I originally wanted to obtain a structural connectivity value from the source region to the all other regions of atlas.