Defining seed , target and waypoints for tractography

Dear all,

I am new to MRtrix3, I would like to know if there is any similar method to probtrackx2 for defining seeds,waypoints and target regions with adequate thresholding in MRtrix. Could you please guide me with some examples.

I have my own seed regions which i have obtained for through segmentations ( Subfields of Thalamic Nuclei ) and i would like to understand ipsilateral and contralateral pathways emerging from thalamic nuclei crossing through way points (pons,hippocampus) and ending in brain stem.



You’ll find the options for seeding here, and the options for include/exclude regions here. As an example:

tckgen wmfod.mif mytracks.tck -seed_image nucleus1.nii -include waypoint.mif -include targetROI.mif -exclude nogo.mif 

That should get you started. If you have more detailed questions, feel free to ask.

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Is it necessary that seed files should be in Diffusion space,also is there a way to threshold the data .

I would like to do group analysis,once i generate individual tracks from each of the subject can i combine all the tracks.

No, all the processing is done in real/scanner space. You can define ROIs on the high-res anatomical or whatever other image you want.

mrthreshold is the simplest, and if needed you can use mrcalc for more complex operations.

There’s different ways depending on what you want to do. One option is to map the streamlines to an track density image (TDI) using tckmap, then warp all of these images using whatever registration program you normally use. Another option is to warp the tractograms themselves to some common standard space, as discussed here. Yet another option is to use tcksample and tckresamplesome discussion on that here. There’s probably other ways to combining the streamlines too, it really depends on precisely what your research question is…

How many -seeds number do i have to set, if i do not set any stream number it goes indefinitely .

Is there any number you recommend , when i use 1million as seeds number, it can only generate small number of fibers