Using clip_edges=True for tract profiles while preserving full bundle visualizations

[TalOhevia]

Hi everyone,

Thank you for your time and help.

I am currently using pyAFQ 3.0 with QSIPrep and MRtrix3 tractography.

Is there a recommended way to compute tract profiles using clip_edges=True, while still exporting the corresponding full (unclipped) bundles for visualization and QC?

If we run the segmentation twice (once with clip_edges=True and once with clip_edges=False), the outlier cleaning behaves differently and we get mismatched streamline counts.

I would appreciate any advice on the best practice for this workflow.

Thank you very much,
Tal Ohevia

[36000]

Hello Tal,

You are correct that the cleaning will produce different results based on whether there is clipping or not. There are a few ways you could try to work around this using the current pyAFQ outputs, but I think it is much easier for me to add a flag to pyAFQ to allow cleaning to optionally use the entire streamlines, even when clip_edges is true. I did that here: #201

Would you mind testing this for me? You can install it via:
pip install git+https://github.com/36000/pyAFQ.git@allow_fullcleaning_clipping

And then set, in segmentation_params, clip_edges=True and clean_unclipped=True

Best,
John

[TalOhevia]

Hi John,

Thank you so much for implementing this so quickly! I really appreciate it.

I'll test it next week and let you know how it goes.

Best,
Tal