pyAFQ default settings for ODF

Hi everyone!

Happy new year! I have been using pyAFQ for my project. I saw on the newest version of pyAFQ (1.1), it says the default ODF method is ‘dti’, not CSD. However, when I look at my .trk file outputs from pyAFQ, it looks like it may have used CSD. For example, my file names are “sub-xx_ses-xx_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-SLFR_tractography.trk,” where it says model-probCSD. Does this mean anything? Or was the default ‘dti’ still used as the odf method (I did not change the odf method from default).

I would be so appreciative if anyone had any insight into this topic.

Probablistic/CSD is indeed the default (see: Could you tell me where in the documentation you see DTI mentioned as the default? We should fix that. Thanks!

Hi Dr. Rokem,

Thank you so much for responding to this comment! That is great news and very helpful. On the documentation GitHub for pyafq version 1.1 release (Releases · yeatmanlab/pyAFQ · GitHub), I downloaded the source code zip and opened the pyafq_cli.json file, and in there it says

        "id": "odf_model",
        "name": "odf model",
        "type": "String",
        "value-key": "[ODF_MODEL]",
        "value-choices": ["DTI", "CSD"],
        "default-value": "DTI",
        "optional": true

That’s where my confusion came from. Thank you so much for clarifying!

Yes. That is confusing. But I think that you can safely ignore that (and we might remove this file altogether soon: Remove pyafq_cli.json · Issue #1082 · yeatmanlab/pyAFQ · GitHub)

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