About Tractography options

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    • #209
      LucaF
      Participant

      Dear all,
      Can I found in the web site (or papers) informations about tractography options?
      For example differences between Multi-Thread and Sort traks, or raccomanded parameters (angle threshold, FA thresohold, GFA/l2 and so on) for HARDI and DTI?
      Thanks
      Luca

    • #211
      David Shattuck
      Keymaster

      hi Luca –

      We are in the process of putting out a new release this week and will be updating our website to match. We’ll be updating the sections on tractography.

      The option for multi-threading means that BrainSuite will run parallel jobs for finding the tracks. If you have a CPU with multiple cores, then this will speed up the computation. For example, if you have a quad-core hyperthreaded CPU, then BrainSuite will launch 8 threads for the computation, and it will be about 8 times as fast. One side effect of the parallel computation is that the order in which the tracks are found is non-deterministic. This is why we have the sort option — it reorders the tracks to be consistent with the single-threaded version. The track order probably has no effect on most applications, but it is useful if you want to compare processing, e.g., compare results from two different computers (we use this to test Mac vs. Linux vs. Windows).

      Many of the other parameters may be dependent on your own data. The angle threshold controls how much the tracks can bend at each step, so how you set this may depend on the anatomy you are studying. Increasing it may produce extraneous tracks. The FA threshold is useful for constraining the tracking to the white matter when computing tracks in DTI; similarly, the the GFA/L2 threshold can be used when using the ODFs. You can use the mask tool to explore the effect of different thresholds on the boundaries in your image. For the FA threshold, you might try a range between 0.1 and 0.3.

      thanks,
      David Shattuck

    • #214
      LucaF
      Participant

      Dear David,
      Thank you very much for your sugestions. I’m processing DWI data from 64 directions, so I will process it using ODF and HARDI.
      Luca

    • #263
      LucaF
      Participant

      Dear David,
      in our previous conversation you have mentioned about a new realease…you said: We are in the process of putting out a new release this week and will be updating our website to match. We’ll be updating the sections on tractography.
      So, is there any news about that?
      Sincerely
      Luca

    • #1554
      shek
      Participant

      Dear experts,
      I am new for using Brainsuite.
      I want to calculate tractography and connectivity by using brainsuite GUI.
      First of all, I did cortical surface extraction sequence.
      Then I opened DTI file to do tractography, but I could not do it because I got this error “No ODF file have been loaded “. Could you please kindly guide me how I can create ODF files? or how I can process ODF files by using Brainsuite GUI?
      All the best
      Fatima

      • This reply was modified 2 years ago by shek. Reason: FORGOT TO WRITE SOMETHING
    • #1830
      Anand Joshi
      Moderator

      Hi Fatima,
      Please take a look at BrainSuite diffusion pipeline:
      http://brainsuite.org/processing/diffusion/

      Here is a step by step tutorial on how to use it.
      http://brainsuite.org/quickstart/dti/

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