Hi Philipp, by default, those parameters are not used anymore as we are using ANTS N4 (though this is not obvious). There is no separate parameter set for for 3T for N4. It is still  possible to use the old MNI N3 code, so we have kept it in there.

On 2/25/2023 2:58 PM, Saemann, Philipp wrote:

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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

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