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[FIX] Updating DIPY tracking params #911
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Since we are using DIPY's local tracking with |
One thought regarding this is that we could verify what we think is correct by running this version on some data and then looking at the distribution of streamline lengths measured in mm. We can get that by taking the point-by-point Euclidean distance between nodes in each streamline, after transferring the streamlines to the RASMM space, where things should be, well, in mm. Then, we can ask what is the maximal length of the streamlines in the whole-brain tractography and see where the distribution cuts off. A bit empirical, but might serve to validate our reasoning. WDYT? |
OK, I think when I was checking lengths earlier I was not using the fix. With the fix in this PR, the HBN work with the matlab default max length of 250 and min length of 50. Will push that change and let's see if the automatic tests agree. |
I think part of the confusion here was I was looking at just a bad HBN subject. I think the current setup should work, though 🤞 |
@arokem this is ready for review / merge. |
I am not sure that I understand what the conclusion of the testing you did was. Does the distribution of streamline lengths curtail at 500 steps (250mm)? |
Yes, it looks like there are very few streamlines longer than 500 steps / 250 mm |
I am still a little confused by what the parameters input to DIPY's tractography algorithm means in terms of units. For example, a max length of 250mm causes problems for many bundles in HBN, however that should be long enough for a typical brain? This was triggered by lowering of max length from 1000mm in recent PR.