Hi Saad,

In the end i could load the matrix with all the fiber counts per pair of voxels (fdt_matrix3.dot) but the intensity of the target mask voxels (4th column of coords_for_fdt_matrix3) is always 0 so i couldn't use your code.

Do you know why the intensity of the target mask voxels is not picked up? Does it need to be numbered from 1 to N? The intensity range is currently composed of non-sequential integers.