Hi Grant That's pretty surprising. If you tar and gzip that whole subject's dir I will take a look
Cheers Bruce > On Apr 12, 2016, at 11:03 AM, Grant O'Brien <grant.o.br...@duke.edu> wrote: > > Hello, > I’m an undergraduate at Duke University working on a study of pediatric > structural imaging. We’ve recently come across some segmentation issues with > the left thalamus (and very rarely the right thalamus) on many of our scans. > Although our study isn’t looking at the thalamus as a region of interest, > we’re concerned that it could be indicative of more global segmentation > issues. > > Freesurfer appears to be incorrectly labeling segments of the left thalamus > as “left cerebral white matter." We initially thought that perhaps the errors > were due to motion artifacts, but we have observed this phenomenon in some > scans with striping and some scans without striping (as demonstrated in the > two screenshots). > > My questions are: > What could be the possible reasons for this incorrect segmentation? > Would scans with this problem need to be excluded? > What steps could we take to fix it? > Why might it only be occurring in the left thalamus? > > Thanks so much for your help. > > Best, > Grant O'Brien > Duke University Class of 2017 > 704-467-5449 > > <thalamus issues + striping.png><thalamus issues no striping.png> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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