Probability maps in qsirecon pyafq pipeline

[Nick_Wellman]

Summary of what happened:

Hi there. We are using qsirecon with the mrtrix_pyafq_tractometry option in our dataset and we noticed that the outcome is different than when we run pyafq from the command line. We noticed we don’t see the probability maps in our output from qsirecon but we do when running pyafq config.toml (for example, *_space-subject_desc-RightArcuateprob_map0_mask). The tract output is different between the two options and we’re wondering if the presence of probability maps is causing this discrepancy. Does the qsirecon pipeline use probability maps for bundle recognition and cleaning? If not is the pipeline using some other method for this process?

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

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[Steven]

Hi @Nick_Wellman and welcome to neurostars!

In the future please use the Software Support post category and template to organize your post and provide us with helpful information. You can see I edited your post for you this time.

@Nick_Wellman

We are using qsirecon with the mrtrix_pyafq_tractometry option in our dataset and we noticed that the outcome is different than when we run pyafq from the command line.
…
The tract output is different between the two options and we’re wondering if the presence of probability maps is causing this discrepancy.

Are you using the same tractography for both? Same PyAFQ versions? If not, that will explain some of the difference.

@Nick_Wellman

We noticed we don’t see the probability maps in our output from qsirecon but we do when running “pyafq config.toml” (for example, *_space-subject_desc-RightArcuateprob_map0_mask).

The probability masks are not saved out by QSIRecon.

@Nick_Wellman

Does the qsirecon pipeline use probability maps for bundle recognition and cleaning? If not is the pipeline using some other method for this process?

QSIRecon is using default pyafq parameters / processes for the most part, with the exception of the MRTrix tractography input in this case. You can see parameters here: qsirecon/qsirecon/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.yaml at main · PennLINC/qsirecon · GitHub

Best,
Steven