pyAFQ default settings for ODF

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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.

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Probablistic/CSD is indeed the default (see: https://github.com/yeatmanlab/pyAFQ/blob/master/AFQ/tractography/tractography.py#L32-L36). Could you tell me where in the documentation you see DTI mentioned as the default? We should fix that. Thanks!

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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!

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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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