Comparing two QSIRecon Workflows using DSI Studio

[Catalina Andrea Saini Ferrón]

Hello,

We have successfully preprocessed dMRI data using QSIPrep. We are now using QSIRecon for reconstruction.

We want to know in which ways we can systematically and quantitatively quality control and compare the outputs of amico_noddi and dsi_studio_autotrack using DSI Studio (latest update). Amico_noddi outputs a fib file, while dsi_studio_autotrack outputs a fib file and also a tck file, per session per subject.

- We tried using DSI Studio's automated quality control of fib files, but it outputs an empty table. Is there another way to quality control these files?

- When running fiber tracking in DSI Studio for amico_noddi fib files, the output tractography requires a manual increase of the tracking threshold, because it looks too "fuzzy" (see example: https://dsi-studio.labsolver.org/doc/gui_t3_whole_brain.html). The recommendation is to "select the lowest value that has acceptable spurious fibers". Is there a way to quality control that doesn't rely only on visual inspection? How can we measure the number of "acceptable" spurious fibers?

- dsi_studio_autotrack output .fib and .tck files seem alright upon visual inspection. However, we would like to compare them to those of amico_noddi quantitatively. What parameters should we be mindful of?

Any suggestions or links to literature would be highly appreciated. We can also share snapshots of the output tractography files when necessary.

Thank you,

Catalina

[Frank Yeh]

Hello,

We have successfully preprocessed dMRI data using QSIPrep. We are now using QSIRecon for reconstruction.

We want to know in which ways we can systematically and quantitatively quality control and compare the outputs of amico_noddi and dsi_studio_autotrack using DSI Studio (latest update). Amico_noddi outputs a fib file, while dsi_studio_autotrack outputs a fib file and also a tck file, per session per subject.

- We tried using DSI Studio's automated quality control of fib files, but it outputs an empty table. Is there another way to quality control these files?

Usually we apply QC on the SRC files, not the FIB files.

For QC FIB files, it may not work for your case because the FIB files were not generated by DSI Studio (some critical information might missing)

- When running fiber tracking in DSI Studio for amico_noddi fib files, the output tractography requires a manual increase of the tracking threshold, because it looks too "fuzzy" (see example: https://dsi-studio.labsolver.org/doc/gui_t3_whole_brain.html). The recommendation is to "select the lowest value that has acceptable spurious fibers". Is there a way to quality control that doesn't rely only on visual inspection?

SRC files or FIB files generated by DSI Studio may provide this function, but may not work for those generated outside DSI Studio.

How can we measure the number of "acceptable" spurious fibers?

I would use pruning or trimming to remove noisy tracts and see the ratio of them.

- dsi_studio_autotrack output .fib and .tck files seem alright upon visual inspection. However, we would like to compare them to those of amico_noddi quantitatively. What parameters should we be mindful of?

As long as the same working parameters are used, I don't see this would be an issue.

Any suggestions or links to literature would be highly appreciated. We can also share snapshots of the output tractography files when necessary.

I am not sure whether using fiber orientations from noddi is good. Most tractography studies are not doing the task this way.

Best regards

Frank

Thank you,

Catalina

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[Catalina Andrea Saini Ferrón]

Thank you for the reply. I will review the files using the information you have provided and keep the recommendations in mind.

Best,

Catalina