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yeatmanlab / AFQ

Automated Fiber Quantification
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Change to mrtrix defaults #31

Closed jyeatman closed 5 years ago

jyeatman commented 5 years ago

The defaults and commands for mrtrix have changed. Thus we need to udate the interface. The major changes are allowing hte user to set the threshold for terminating tracking and set the response function. Default thresh is now set to 0.1 which is different than the past but was needed to get decent results. This should be investigated to set optimal defaults that will work for a range of use cases

mayayab commented 5 years ago

Several issues I noticed:

  1. In AFQ_Create, lines 229-233 should be moved after the block that sets the parameters for mrTrix, otherwise the defaults override the user input.
  2. The default lmax is 6 in AFQ_mrtrix_response, but 4 in AFQ_Create and AFQ_mrtrixInit. I think it's better to stick with 4 as it is compatible with more datasets? Gari, what do you think?
  3. The default cutoff is set to 0.1 in AFQ_Create but 0.05 in AFQ_mrtrix_track
jyeatman commented 5 years ago

@mayayab I made your proposed fixes - will you check that it works as expected? And let me know if there are other changes that should occur while we are on this