Hi Saad,
Thanks, it's good to know the fact only the upper half is stored is on purpose.
As shown by the output path distribution (myoutput.nii.gz in the files i sent you) all white matter is covered by samples and these samples reach all target ROIs, while most entries are still zero in the connectivity matrix:
- could that be that the stop mask being the same as the target rois then the tracts are truncated before reaching the targets?
- since i'm seeding from the GM/WM interface and the targets cover most of the GM, could that be that seeding from the interface all "one-voxel step" directly ending in one target make the tract not being counted somehow (again due to the stop mask)?
Because the samples cover the whole brain i'm not sure increasing their number would change these results but i will run 10 times more samples to check, say 100 (usually i can get the usual connectivity matrix pattern after 10 samples per voxel with whole WM/GM interface seeding).
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