Resampling to 30 nodes using pyAFQ config file

Software Support
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1

Summary of what happened:

I’ve been trying to use the generated config file from pyAFQ and it works but I would love to resample down to just having 30 nodes across each tract instead of the default 100. The config file runs just fine but I can’t seem to get the amount of nodes to change no matter what input I adjust. I’ve seen this mentioned as an option in the API on the tutorials (AFQ API — AFQ 1.1 documentation) but was wondering if it was possible to do using just the config file through the CLI. I’m currently using the dev version of pyAFQ but have tried on both versions with no success. I’m hesitant to make the commitment over to the API but maybe that is the best option?

Command used (and if a helper script was used, a link to the helper script or the command generated):

# Number of points to resample streamlines to.
# Default: 100
n_points = 30

This was the code in the config file I assumed would adjust the nodes. But didn’t seem to help.
Hoping this is something simple I’m just totally missing! Thanks for any help or advice and sorry in advance if my post is not formatted correctly, I’m very new :slight_smile:

2

Hello @danaparker and welcome to Neurostars!

The current version of pyAFQ does not allow you to use any other number than 100, but … a future version will, because that’s a good idea to let users do this.

The section that you are referring to in your question only applies to the portion of the pipeline where cleaning of outlying streamlines is conducted, and gives the user control over the sampling of streamlines at that point (and only at that point).

I will say that for now my guess is that a moving average over the 100-point profile would probably produce something very similar to what you would have gotten if you used 30 points instead, at least in the central portion of the profile. But I have not verified that.

I hope that answers your question!

Ariel