Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance!
Tudor On 5 July 2013 17:26, Tudor Popescu <tud...@gmail.com> wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I noticed that there are artefacts (chips) in the brain-extracted > structurals of several of my subjects. Since I ran recon-all on all my > sample without having noticed this initially, this of course also lead to > the surfaces being created wrongly, i.e. following the wrong volumetric > information. > > I attach screenshots showing some of the more obvious artefactual skull > extractions, corresponding to subjects 04, 06 and 17, and also the > brain.mgz and T1.mgz for subject 17. > > FSL's BET extracted the skull with no problems from the same original > structurals, so I'm guessing it's maybe the case that I need to override > some parameters in recon-all in order for the initial recon-all to produce > good brain extractions? > > And by the way, I noticed that, in any one subject's folder, the images > /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the > subject's original structural scan. Why does this exist in 3 separate > copies, which also seem to be of different file sizes? The only difference > I can see between them is in terms of brightness correction... > > Many thanks! > > Tudor >
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