We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:

• In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly.
• However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all  -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction:
• In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not.  We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script.
• When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. 
• Below  are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:

 

mri_nu_correct.mni.log:

...

/usr/local/freesurfer/bin/mri_nu_correct.mni

--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50

nIters 1

mri_nu_correct.mni 7.1.1

...

AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz

Using shrink factor: 4

...

 

 

 

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Christine Fennema-Notestine, Ph.D.