External Email - Use Caution Hi Varun,
I’m not sure what issue that you have been running into. Can you send your recon-all.log? In general, you need to 1. set environment variable SUBJECTS_DIR to some directory that you have write permission 2. pass full path to T1 image to -i <full_path_to_T1_image> Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Varun Chandran Sent: Wednesday, June 21, 2023 10:32 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Pial and White surface maps are not found External Email - Use Caution Hi FS experts, It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light on this issue? command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache thanks, best, Varun -- Varun Arunachalam Chandran, PhD Postdoctoral Research Associate, Faculty of biology, medicine and health, School of health sciences, University of Manchester, United Kingdom. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1bHhTXwdOESSJfYuD_YXb0duh_c6zpNTYzxdPW3Tvj__fap_JYjIqU97JG3npPScMbiMRUNjt28oX5aE-NrEwM7ElsWZydkf4hIKJb9k6iNRJjsQp_ZmIqNgtfFW0yOEWt5aiZ42jpce0A2DKLadAx3sJYPILUL8m38RGOyB-WzJr0dLkVICRTbxTP7k6DY3w-LwMbjmZuySnDfoi_BONyMTn3J0BeD8wA2AZDhfybXW2YKAs-YbJ20gJM6azm0F7iV8oidiS7y1koHmpBrtYIA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F<https://secure-web.cisco.com/1cnuenNM09eOjp8mrBzh-QGzKlgQQ0c8Rw7bNumyV-qFdkCjJPaU7LXYRxKGgbYxUiRXi5zKScT5gHmVubIUvIUpsPPuJKYBPYb_HvYI02KUmRTUjZN_AtsagwYGP1pqFwfThhqJzeoAwW5vW-rIS2c23JlIQc8TSb27qeu7ZKdzERpB1pZzxuqUfgJuv4jA0o3BBdnDICJEgOPcUcYjbYS5eLXVgmkvLtU-PoHVJRjCAiH-vUxn3hP6EAhuIxa7DOtcbhEy2VZVoF5ADRqVWhwvxjs7pXFwpB5rA8kzvx97Uh4_4nLhM1JhURLJWtUxl4THj_dQ2B6bNbuyayXzQLw/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F>
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