Tckgen can't find many streamlines

1

Hello MRtrix community

I’m trying to use tckgen to find streamlines, for example between Straiatum and DLPFC:

tckgen MMSP01/MMSP01_FOD.mif MMSP01/MMSP01_tract_NMM_DLPFC_L_FLIP_NMM_STRIATvent_L_FLIP.tck -algorithm ifod2 -seed_image MMSP01/wROI_NMM_DLPFC_L_FLIP.mif -mask MMSP01/MMSP01_brainmask.mif -include MMSP01/wROI_NMM_STRIATvent_L_FLIP.mif -exclude MMSP01/wmwc301_T0_MPRAGE_BIN.mif -step 0.2 -select 5000 -stop -seed_unidirectional

However, tckgen only generates between 1 to 250 streamlines before reaching the limit of 5000000 generated seeds. Using maxnum to reach the goal of 5000 streamlines would obviously also increase the calculation time needet drastically.

Do you have any suggestions?

Thanks

Leo

1 Like
2

Hi Leo,

Have you checked your masks (all inclusion and exclusion)? Can you share them visually? It happened to me once, and I realized that my inclusion mask was not that much inclusive. I suspect that your “exclude” mask has a huge overlap with your inclusion masks or the streamlines connecting the two regions.

Best,
Amir