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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