External Email - Use Caution Hello Varun, The Windows file system, i.e., NTFS, does not support soft links. So you cannot set SUBJECTS_DIR to storage mounted from your Windows machine that has been formatted by Windows OS, and then run something in the linux VM that is going to try to write and create a soft link there, e.g., if that is what /media/sf_VBOX/T1_FreeSurfer is set to point to via SUBJECTS_DIR. Anything that writes and creates a soft link running in the linux VM needs to write directly to the linux file system inside the VM. - R. On Jun 21, 2023, at 11:55, Varun Chandran <varunchandra...@gmail.com> wrote: External Email - Use Caution p.s. I am wondering whether this specific issue arises while working with freesurfer using Linux based Virtual Machine? On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran <varunchandra...@gmail.com> wrote:Hi YujingThank you very much for your quick reply. Yes, I used a directory path to set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the 'recon-all' command line. However, it was not very helpful to obtain the pial and white surface maps and exited with some errors as shown in the recon-all.log (please see the file attached). Now, I'll try running the same command by entering the full path name of the directory as you suggested. thanks again,best,VarunOn Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: 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 to1. set environment variable SUBJECTS_DIR to some directory that you have write permission2. 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 ChandranSent: Wednesday, June 21, 2023 10:32 AMTo: 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, PhDPostdoctoral 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/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNfr9E_ne8XOT8k6h73dsLYwBJCchau9Jn6Nrmm5VwrWL6RynB4rHm_gl_OFy0IKNMLKNiAHRNlbZp1vFG2WPmH_ADuYHlev5XaaTpxAcelJVQLtnkZBp0MsffsqimUYx54CC1IrcB1Yf0k9_suDatbprPu4NoU0w0YIb8JQ-Dmzif8hbd0-AMzj5PQyZOTTM0XMw3C9k36QGNmZec0MZqWLbqJq6SM9yGIcoFjPnNBcX-cDSoBwiky8BWPyzkjXHYuESyHmZBIiU0bh3hzLdHj4N2S2MC3R3XsTYMWRnp3P_SMA79Gg/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZXw_kqqZ3KZ69Di0XOLR2y7cRSFo0QTVxLkueLM8jdls7aOr2XpVPCM6VC31M_FkX1_7vqCXscyJlfrMnCJsUlaMd49-FlWgH2l_E4Sm92x9RU82T7nefjYL92dkRTS_j1aDOK-M1_zHgItz0xDEFZ8hx8Ga6l-d-30x_icYnzboV-R2BiJFc79tp9RxcjwVbZDDM_OQyHejkBa5NWyV9HjFnjwumAHAFuDxWcU8VXfSGV0Imn6bMSufMo5nV_zzyqCGE0sKykbHsxArl45PPmf7rfD8ggXefbYqwSqoRl4Nvgo8Js91yj-bBT1jxBkegQgSSqyMgUpxcN7ruZ1nhw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26nbsp;<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oLoAtw1TpZh6szgfCA5qRM4stI7vUsPUnYCur1XSVBMdlu9j0QjEiBoOcesYULmvBIiWHa9pHgq9C8qEqn0xhZkw66ayfvYb4K_LLI3HSUlh9DwppUR9GkM2IHxq1K7P7UcsheqpG4oQfBd3bumqWzHdQd3C1-4KOKTD5EV2dCbDOMjG4-3gAMyttGgyuW3xYLVYbtzwKSQsAqaha0RhpxZQPxgeGP_NXfvZLYftIXjCqUaaYbtU9oRaCG3s57iOKYL9l-9MdjCLEg1DUDZsCgssnKAPHzWWVXqcSbsYgsv_xEtOWcvs52k6AN47J9FRkVkUEDhODMk8HHR4stef6A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; .-- Varun Arunachalam Chandran, PhDPostdoctoral 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/1i4aoGzHc6a0AY8hqw5Q4UmY5qB-iVj7FH4bDeAZJwUd0EqsofbcHJFQKsZA8pliPrn5CHBiVDJarY0T_GfdrAaabRRvmC_p0wzW7ORPTFy2Dvx27KRNK67Ue7-ae4-YDVyWL9n6BYu9dCYR1tCHqNv8GFulEYhgns8fYBqz4yEG1xqEU7LIm9lHcDL3Grm-2dZYRnkIVUPqDvQ7y9NrvrPa_VsVr-3bLLyBEHGLYL3ekVtgk3xB_3qd0NtBssoR61zc74EIaNVGu6DYEBUJGXqh1CekdCL-VELVB0QELZlSGYuCskRuNiutP4N-EB7tZ4bXFXaRUglLpHs2ImQk5sw/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F--%26nbsp;Varun Arunachalam Chandran, PhDPostdoctoral 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/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNfr9E_ne8XOT8k6h73dsLYwBJCchau9Jn6Nrmm5VwrWL6RynB4rHm_gl_OFy0IKNMLKNiAHRNlbZp1vFG2WPmH_ADuYHlev5XaaTpxAcelJVQLtnkZBp0MsffsqimUYx54CC1IrcB1Yf0k9_suDatbprPu4NoU0w0YIb8JQ-Dmzif8hbd0-AMzj5PQyZOTTM0XMw3C9k36QGNmZec0MZqWLbqJq6SM9yGIcoFjPnNBcX-cDSoBwiky8BWPyzkjXHYuESyHmZBIiU0bh3hzLdHj4N2S2MC3R3XsTYMWRnp3P_SMA79Gg/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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