Hi - See my answer to Knut Jørgen about the isosurfaces. I forgot to answer the second part of your question: the outliers of the -stat step are tracts that have a very different shape from the rest, so you can check those and see if they failed, but hopefully any QA/reinitialization would have happened before the -stat step, because that step is not really designed right now to pick up everything that could've gone wrong with the data.
Best, a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lars M. Rimol [lari...@gmail.com] Sent: Saturday, November 19, 2016 5:37 AM To: FS maling list Subject: [Freesurfer] quality control of tracula tractography Hi, I have done tracula tractography on 180 subjects, and most of my isosurfaces look a lot noisier than the example on the wiki. Is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? For instance, here (https://neuro.ebioscience.amc.nl/portal/web/nsg/tracula) they do not accept a somewhat noisy fminor. Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (see attached figure, which was not flagged in lh.cab_PP.avg33_mni_bbr.log) - but they may fall under the minimum threshold and therefore not be evaluated? Is it recommended to automatically exclude the subjects that are flagged as outliers there? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway
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