External Email - Use Caution Hi FreeSurfer specialists,
we have problems with a strong non-intensity in 3 Tesla data of GE (mainly temporal poles and occipital area). We managed to rescue the occipital errors by a pre-Bias-field correction using SPM, but would of course try to optimize this in recon-all itself. When I open the recon-all scrip tin FS v7.1.1 I can find no difference in the parameters depending on if the the flag "-3T" is set or not. In both cases the parameters forwarded are: --n 1 --proto-iters 1000 --distance 50 (in line 1536 and line 1540 of /bin/recon-all.) Could someone explain this? What could be done (manual corrections etc. are obsolete due to the large sample size...) to improve the WM detection in the temporolateral/polar area (subsequently cortex detection)? The brainmask looks okay; the ribbon.mgz shows the cut off lateral parts of the cortex. Thanks in advance for any hints, Philipp
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