Seed-based tractography

Hi,

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.Method_01

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.

2.Method_02:

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.

Thanks,
Thomas

Hi Thomas,

1.Method_01
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

:no_good_man:

You cannot apply the model underlying SIFT to the output of a targeted tracking experiment; it can only be applied to a tractogram that includes the reconstruction of all plausible pathways. In retrospect I failed to adequately assert this in the corresponding manuscripts…

E.g. Consider a voxel where just one streamline from your targeted tracking experiment traverses, but if you were to do whole-brain tractography, you could see that that voxel is predominantly traversed by other white matter pathways. If you were to apply the model underlying SIFT to just the targeted tracking reconstruction, it would attribute all of the fibre density in that voxel to the pathway of interest, which is clearly not reflective of the underlying reality.

2.Method_02:
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.

If you are interested only in the connectivity between node 146 and every other node in the parcellation, why not just manually extract line 146 from the full (symmetric) connectivity matrix, and completely omit steps 4 and 5? It seems to me that step 3 already generates the data you want, and steps 4 and 5 are a very convoluted way of trying to access the specific subset of connection strengths in which you are interested.

Rob