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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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...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