Question about the autotracking

[yh]

Hi Frank!

  I got a few problems wants to get help from you:

1 If i want to find difference between left and right middle cerebellum peduncle, such as mean FA and shape analysis measurement, is it approprate to cut the exist template(middle  cerebellum peduncel) into left and right part and save them as tract template of left middle  cerebellum peduncel and right middle  cerebellum peduncel?

2 I want to get fiber connection between red nuclear and cortex just like potine and cortex, Is it approprated to manually tracking these fibers in you hcp1065 1mm population  averaged template and save them into the all tract template in autotrack function ? if so,  what is the difference between already exist template and template that i added?

3 continue with problem 2 , I  have read related  introduction about how autotraking was achived. but i still cant fully understand how it achive best performance in pruning fiber, automaticly using TIP? If so, the tract template that i added will not be pruned? but  if i manually edit the tract in the process of tract template making, will it pass to the autotracking process?

4 Why there was no occipital-potine tract in cortex potine fiber?

5 How you can distinguish cortex-potine tract with corticospinal tract,both of them start from cortex and path through potine? By setting potine as end and ROI?

[Frank Yeh]

  I got a few problems wants to get help from you:

1 If i want to find difference between left and right middle cerebellum peduncle, such as mean FA and shape analysis measurement, is it approprate to cut the exist template(middle  cerebellum peduncel) into left and right part and save them as tract template of left middle  cerebellum peduncel and right middle  cerebellum peduncel?

I would use a region atlas instead of tractography. You can use [Step T3a][Atlas][HCP842_Tractography] to get the region and extract value directly.

 

2 I want to get fiber connection between red nuclear and cortex just like potine and cortex, Is it approprated to manually tracking these fibers in you hcp1065 1mm population  averaged template and save them into the all tract template in autotrack function ? if so,  what is the difference between already exist template and template that i added?

The pathway you are looking for is the cortico-reticular pathway, which is included under the [reticular tracks] in the current auto tracking list (most recent version).

I will use it and combine [Step T3a][Atlas][BrainSeg][Red Nucleus] added as an additional ROI to narrow down the tracts.

 

3 continue with problem 2 , I  have read related  introduction about how autotraking was achived. but i still cant fully understand how it achive best performance in pruning fiber, automaticly using TIP? If so, the tract template that i added will not be pruned? but  if i manually edit the tract in the process of tract template making, will it pass to the autotracking process?

You can manually apply TIP by [Edit][Pruning] (If I understood your question right)

  

4 Why there was no occipital-potine tract in cortex potine fiber?

The list has [Corticopontine_Tract_Occipital]

 

5 How you can distinguish cortex-potine tract with corticospinal tract,both of them start from cortex and path through potine? By setting potine as end and ROI?

Their trajectories near the cortex are very different, but the location downstream below the midbrain has substantial overlap. Any region setting at pon may not be good enough to distinguish them.

Best,

Frank 

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[yh]

Hi Frank!

    I have noticed a error in my Q4,  it should be " i cant find  [Corticopontine_Tract_Temporal]". Maybe no fibers origin from temporal lobe to potine? 

Best,

HuYin

[Frank Yeh]

This pathway is hard to map in some subjects.
Frank

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