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Dear all,

I'm new to freesurfer and I'm trying to preprocess a 7T mp2rage dataset (0.6mm³ isotropic, TR=6000ms, TE=2.05ms) with freesurfer 7.2.0.
The images have been corrected for B1, for intensity inhomogeneity with ANTs N4 bias field removal and they were skull striped with FSL based
on intensity. This was done by a colleague who analyzed  this dataset in 2017 and I'm hoping to run our updated toolboxes on the preprocessed
data. However, he ran into several problems while first analyzing the data: freesurfer did not like the noisy background of the mp2rage, which is why
he skullstripped the data before preprocessing it with freesurfer. He then ran recon-all once with the default pipeline and once with skull strip deactivated.
According to him, the default pipeline yielded better results. I'm using his skull-stripped data now for the preprocessing and was wondering whether not
deactivating the skull strip will lead to inaccurate measures for cortical thickness and gray matter volume. Since this is crucial for our toolboxes, we really
want to be sure that we're going for the best solution. A second problem is the high resolution of the data - it's not recommended to run the default recon-all
on anything lower than 1mm³ (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon), but most of the information I could find is from 2016 or 2017.
At the time, he used the -hires flag but got very bad results, which made him use the default pipeline even if the mp2rage data got downsampled. I was
wondering if anybody has feedback on how they analyzed a similar dataset (high resolution, problems with skullstripping etc.), general opinions on the best
way to analyze this dataset and/or if there have been any developments (e.g., new flags for recon-all flags?) that I'm not aware of. We got feedback from
one colleague that they did analyze their dataset successfully with the -hires flag and did not encounter any problems at the time. Any advice would be much
appreciated!

Best and thanks in advance,

Sabrina

-- 
Dr. Sabrina Turker (she/her)
Postdoctoral researcher 
Brain and Language Lab
Department of Behavioral & Cognitive Biology
University of Vienna