I’ve since rethought my strategy, since I am not sure what I was describing first would be feasible or be the best route given the goal of the analysis. That is, using the full premade tractogram would both render it hard to associate streamlines with origin voxels and leave no way to ensure that each voxel was seeded the same number of times. Both of these confounds would work against the planned analysis.
Essentially, I am trying to do this, but with QSIRecon/MRtrix tractography. I already have the DWI-registered parcels for a different atlas:
Automated cortical parcellation was performed in each participant’s T1 scan, using the Destrieux atlas (Destrieux et al. 2010) from Freesurfer 5.1 (Fischl et al. 2002, 2004) to define 148 cortical regions. … We used the DWI-registered parcels as seed and target regions for fiber tracking…The principal diffusion directions were calculated per voxel, and probabilistic diffusion tractography was carried out using FSL-FDT (Behrens et al. 2007) with 5000 streamline samples in each seed voxel to create a connectivity distribution to each of the target regions, while avoiding a mask consisting of the ventricles. Each of the 148 regions was used as a seed region and tractography was carried out to all 147 remaining regions, or targets. Thus, every voxel within each parcel is described by a vector of connection probabilities to each other brain region.
I might redo the tractography, but this time seed particularly from a given parcellation region (in my case, right fusiform gyrus) using the following parameters:
tckgen -act ACT.nii.gz -backtrack -crop_at_gmwmi -seed_random_per_voxel fusiform_R.nii.gz 5000 -include everything_besides_fusiform_R.nii.gz -output_seeds seeds.txt
If I do this, will there be a way to associate streamlines to the voxel they were seeded from? Is that what the -output_seeds argument would specify?
I would hope that FOD power would be low enough in ventricles that I wouldn’t have to worry about streamlines crossing them.
Thanks,
Steven
Post attempt edit: Perhaps I’ve misunderstood how -seed_random_per_voxel, because the number of streamlines I was getting seemed to far exceed the number of voxels in the mask*5000. I also had a chance to look at the seeds output file, and am having trouble figuring out how to use the seed_index field. Would it be best to use the X Y and Z position of the seed to assign voxels?