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 Yujing > > Thank 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, > Varun > > > On 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 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/135dxZwIDQx9bbQ4IxE4063rhuKY-x_fftMMGZfTGtSk_plGZ6LdWEv2ZMYt12IvB3X2dI7Kj8GttX9kMCJBp1qi4SdxkH58VOdWyEUMZx_c6mif50a07j64w0R7sSbKh9Yz4luxB1LEyouFCqruu_ewvGQ09MSvAxdD3bcMqOQqd9zKhKdocmm8HHarkeiHKYmbw5oHd3fXo6iiyNpG1VBo1KeB_FWPlPhXBs9ZoGZyVSNDgTrQA0ah4vMbVlU5pRVaCEdzDrs-aeWGPyJkonK3DxaJ24pxim5jWIwVwsIC3STskjz0hJrrHItjGKlb50sYyUgkrwNBVzcJG56MXyA/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> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1zUAdJsUJNYQqEK7bzUPMGKxVCXRGrCJM3aLdxeUZi3vCMa-t6r4S0uN3tk4Qfy_impRTenB8mTV_fx7BZ56IxxIOCckCUcoQp_3N8PTUQADNalq_fnGTPDKSm7kvj60CGVPNpqEltRJATLP9Ui6-8JCAyC8IHeCWk-Mus2oSlJ7E9wrL4kbdu4QeK_fjA6wzK-IWHI4fAPsMOgJa0IIeGnesNfL_p9r1C7TixN6SyOKNsSxvXxK9uszKIGfiMkuC3QU_11ktpZO2KAS8MuqUq7ujM8_TtICBEDg9oIM3nP1sCIM1yNyIO4yZUWiZNMlIwftyM9SQGK3Ag37cCBtjXQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> The 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 >> https://secure-web.cisco.com/1yxyAHFpw5YAP4A1axp_bsC-f58t9ZmmMWd0LablVhsxQFKTI7fQFECjOqQ6pOe9zpHcxocWLa1Pguza3XntXxoUz4kvMVq0wh2q22COnlBkeG-osRxy5NeXNEq7brYudqEZB1v1NZTivYX-hi2KfMgPPdcP5FeBiXDIt2X2xr7tSrerQgYYUDVFr4PX2BA6UwWEWBOzVTEQfpTzbvMt5XH-w_RG1ynQHC6HodCE1OpZQO-CiBiqVneyg9LtW8z0dT5ILJn_LsGCT8ZYYFXRs_XgSRLmnFWzqvVCsMqxW8GdHVo5xVYIJw3-Gqc4bnQGO89m4dgEhenZLU-_dAr0MDQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> < >> https://secure-web.cisco.com/1yxyAHFpw5YAP4A1axp_bsC-f58t9ZmmMWd0LablVhsxQFKTI7fQFECjOqQ6pOe9zpHcxocWLa1Pguza3XntXxoUz4kvMVq0wh2q22COnlBkeG-osRxy5NeXNEq7brYudqEZB1v1NZTivYX-hi2KfMgPPdcP5FeBiXDIt2X2xr7tSrerQgYYUDVFr4PX2BA6UwWEWBOzVTEQfpTzbvMt5XH-w_RG1ynQHC6HodCE1OpZQO-CiBiqVneyg9LtW8z0dT5ILJn_LsGCT8ZYYFXRs_XgSRLmnFWzqvVCsMqxW8GdHVo5xVYIJw3-Gqc4bnQGO89m4dgEhenZLU-_dAr0MDQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . >> > > > -- > > Varun Arunachalam Chandran, PhD > > Postdoctoral Research Associate, > > Faculty of biology, medicine and health, > > School of health sciences, > > University of Manchester, > > United Kingdom. > > https://secure-web.cisco.com/135dxZwIDQx9bbQ4IxE4063rhuKY-x_fftMMGZfTGtSk_plGZ6LdWEv2ZMYt12IvB3X2dI7Kj8GttX9kMCJBp1qi4SdxkH58VOdWyEUMZx_c6mif50a07j64w0R7sSbKh9Yz4luxB1LEyouFCqruu_ewvGQ09MSvAxdD3bcMqOQqd9zKhKdocmm8HHarkeiHKYmbw5oHd3fXo6iiyNpG1VBo1KeB_FWPlPhXBs9ZoGZyVSNDgTrQA0ah4vMbVlU5pRVaCEdzDrs-aeWGPyJkonK3DxaJ24pxim5jWIwVwsIC3STskjz0hJrrHItjGKlb50sYyUgkrwNBVzcJG56MXyA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F > -- Varun Arunachalam Chandran, PhD Postdoctoral Research Associate, Faculty of biology, medicine and health, School of health sciences, University of Manchester, United Kingdom. https://secure-web.cisco.com/135dxZwIDQx9bbQ4IxE4063rhuKY-x_fftMMGZfTGtSk_plGZ6LdWEv2ZMYt12IvB3X2dI7Kj8GttX9kMCJBp1qi4SdxkH58VOdWyEUMZx_c6mif50a07j64w0R7sSbKh9Yz4luxB1LEyouFCqruu_ewvGQ09MSvAxdD3bcMqOQqd9zKhKdocmm8HHarkeiHKYmbw5oHd3fXo6iiyNpG1VBo1KeB_FWPlPhXBs9ZoGZyVSNDgTrQA0ah4vMbVlU5pRVaCEdzDrs-aeWGPyJkonK3DxaJ24pxim5jWIwVwsIC3STskjz0hJrrHItjGKlb50sYyUgkrwNBVzcJG56MXyA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F
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