# Defining seed , target and waypoints for tractography **URL:** \ **Category:** Uncategorized\ **Created:** [July 17, 2019, 2:56pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682 "2019-07-17T14:56:38Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Vaasudev](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/v/4af34b/32.png) [@Vaasudev](https://community.mrtrix.org/u/Vaasudev)\ **Post date:** [July 17, 2019, 2:56pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682/1 "2019-07-17T14:56:38Z")
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. Thanks Vasudev Thanks Vasudev ---
**Author:** ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)\ **Post date:** [July 17, 2019, 7:40pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682/2 "2019-07-17T19:40:37Z")
You’ll find the [options for seeding here](https://mrtrix.readthedocs.io/en/latest/reference/commands/tckgen.html#tractography-seeding-mechanisms-at-least-one-must-be-provided), and the [options for include/exclude regions here](https://mrtrix.readthedocs.io/en/latest/reference/commands/tckgen.html#region-of-interest-processing-options). As an example: ```auto 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. ---
**Author:** ![Vaasudev](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/v/4af34b/32.png) [@Vaasudev](https://community.mrtrix.org/u/Vaasudev)\ **Post date:** [July 18, 2019, 12:35pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682/3 "2019-07-18T12:35:13Z")
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. ---
**Author:** ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)\ **Post date:** [July 18, 2019, 3:55pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682/4 "2019-07-18T15:55:58Z")
> [@Vaasudev](#): > > Is it necessary that seed files should be in Diffusion space 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. > [@Vaasudev](#): > > is there a way to threshold the data [mrthreshold](https://mrtrix.readthedocs.io/en/latest/reference/commands/mrthreshold.html) is the simplest, and if needed you can use [mrcalc](https://mrtrix.readthedocs.io/en/latest/reference/commands/mrcalc.html) for more complex operations. > [@Vaasudev](#): > > I would like to do group analysis,once i generate individual tracks from each of the subject can i combine all the tracks. 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](https://mrtrix.readthedocs.io/en/latest/reference/commands/tckmap.html), 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](http://community.mrtrix.org/t/warping-tck-files-using-ants-warps/162/4). Yet another option is to use [tcksample](https://mrtrix.readthedocs.io/en/latest/reference/commands/tcksample.html) and [tckresample](https://mrtrix.readthedocs.io/en/latest/reference/commands/tckresample.html) – [some discussion on that here](http://community.mrtrix.org/t/tckresample-and-tcksample-for-along-the-tract-statistics/1368). There’s probably other ways to combining the streamlines too, it really depends on precisely what your research question is… ---
**Author:** ![Vaasudev](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/v/4af34b/32.png) [@Vaasudev](https://community.mrtrix.org/u/Vaasudev)\ **Post date:** [August 1, 2019, 2:12pm UTC](https://community.mrtrix.org/t/defining-seed-target-and-waypoints-for-tractography/2682/6 "2019-08-01T14:12:50Z")
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