Hi Bryna, In this tutorial, it talks about how to fix bad output from the talairach registration:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Goeckner, Bryna Sent: Friday, February 10, 2023 3:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all exited with errors External Email - Use Caution Hi All, I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated. I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white). I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks! The original code was: recon-all -subject subj# \ -i rawT1.nii.gz \ -T2 rawT2.nii.gz \ -T2pial \ -parallel -openmp 12 \ -3T \ -all And for the second run, -notal-check was added after -all For tkregister2: tkregister2 --s subj# --fstal --surf orig Bryna Goeckner (she/her) Graduate Student Meier Lab<https://secure-web.cisco.com/1pur5M1FnQYnB8iXyrOEPR6TC3h-zcLEgSRygNp0xNHDNFaXD1i9-hPhj4Oaq7TDIvti413rNC9uMY0VMqc0BLx51pq_PXmRoypSPWBkRpLmqFydLNzaEPHOdJXWdRLTEUYo5NRJEfXTSdVU7iLzTCc1UQ23ZLxfHhu6BBI7xeykqdgLkfnskuLA9cBN5rareF2ZVEm7EJ1-5SRGPa-Yy-cKtYsSsDZ1ZLu0FpmRYrSft1XWegfp9_r3MB99se6slt5EKoA83CdtSQQYyNW8MwoTzjhQRkYLE2ACGBCiRt8T_cqUCCQN5BsVfpILRu1Pal_d5Y5I6dCqc7jNcZ3PtOQ/https%3A%2F%2Fwww.mcw.edu%2Fdepartments%2Fneurosurgery%2Fresearch%2Fmeier-laboratory> Medical College of Wisconsin Neuroscience Doctoral Program
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