Extract the number of streamlines connecting one voxel with target ROI

Hi experts,

I am now doing probabilistic tractography via tckgen.
I would like to know is there any solution to extract the number of streamlines connecting one voxel with target ROI?
I have read several paper who used the FSL-BEDPOSTX, but it takes very long time for I only have CPU.
I am quite new to FBA, and very thankful for anyone could help.



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Hello Li :slight_smile:

There are different approaches, but basically they involve having two masks - one for your target ROI and one for your single voxel - and using them as include regions.
You could either do whole brain tractography and then filter the result using tckedit e.g tckedit wbt.tck -include voxel_roi.nii.gz -include target_roi.nii.gz voxel_2_target.tck or you could do targeted tractography directly e.g. tckgen wm_fod.mif -seed_image voxel_roi.nii.gz -include target_roi.nii.gz voxel_2_target.tck. Then you can use tckinfo -count voxel_2_target.tck to get the number of streamlines.

The trouble with the second approach (targeted tractography instead of whole brain followed by filtering) is that it’s difficult to ascribe any kind of meaning to the number of streamlines, since it will likely just be whatever value is provided to the -select option (the default is 5000), unless the maximum number of seeds is reached.
So the whole-brain approach makes more sense if some sort of quantification is what you are looking for. If you search this forum for “whole brain tractography” and “targeted tractography” you will find lots of discussion that will explain it better than me! For example here, and this other post similar to yours. It all depends on your research question ultimately.

Hope you are well!


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