On 4/22/2026 12:36 PM, Huaiyu Liu wrote:
External Email - Use Caution
Dear FreeSurfer Developers, I am attempting to preprocess my 7T MP2RAGE UNI image (*0.65 mm isotropic resolution, TR = 5000 ms, TE = 2.54 ms*) using FreeSurfer 8.2.0 with the following |recon-all| command: recon-all -all -i sub-01_t1w.nii -s sub-01 According to a discussion thread I found in the FreeSurfer archive https://secure-web.cisco.com/1LCAbAxlUHY-wISqgMbjgKwSDIJ2615y8K3UxjFEuQ_26m_iFvyq0tg3A9GdTBu_hftOzPDyAXXkWICuBw1qRMUPQ30XZkSJ4kXZJXrCZUGxs9QgMj4xhO36dA4e8g1Ksc1A0o_TqHxAeaXVUCrFaZWW0Kc788ggrultV6j-zHELTl0IPdyh2OIO3WyQB70VHuxgF5i11nC-oIST_2_WsSYe7XwwHOmHDNrNl_A3bBGbsqnVeZ5d69JeyZvqnHUBhB7CAMv3jeEanEXbtcGp91k5L0vsxCvCN9uu5Pgua4GYOr_nrnrHM8T78AMzVhG4-zlH7lLoCWpKulo_4Rn5vaA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg77849.html, it seems that it is acceptable to run the default |recon-all| pipeline directly on raw MP2RAGE UNI images without prior skull stripping.
- May I know that whether this is still the recommended approach for
FreeSurfer 8.2.0?
Yes
- Additionally, if I want to use FreeSurfer version 7, would it be
preferable to perform skull stripping beforehand, or is it still advisable to use the raw UNI image directly?
Yes, that is a good idea
Thank you very much for your guidance and/or suggestions. Best regards, Huaiyu _________________________________________ Huaiyu Liu (Ted)_ _Postdoctoral Research Fellow Department of Imaging Neuroscience, Functional Imaging Laboratory University College London 12 Queen Square, London WC1N 3AR
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