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Hi Freesurfer Experts,

I have run into a problem with several subjects ranging over several different tracts (usually just one tract per subject) where a tract will not display correctly in merged_avg16_syn_bbr.mgz or in the individual pathway (ex: lh.cbv_avg16_syn_bbr/path.pd.nii.gz) without first adjusting thresholds. I also discovered that the volume in pathstats.overall.txt in these cases is significantly higher than the average – on the order of 10 times bigger.

I know there is mention of using “set reinit=1” to repair tracts that are too small or missing. Would this be recommended here as well or is there another better direction to take?

I am including a link to the trac-all.log for a subject whose rh.ilf is problematic. Please let me know of there is any other information you need and thanks for your help! https://secure-web.cisco.com/1-H9YB7x0pcdABFBAqsjeogpPsh-50RChRNS5qTyoP0bcnJ...

Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program