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 archivehttps://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. 1. May I know that whether this is still the recommended approach for FreeSurfer 8.2.0? 2. 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? 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
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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