External Email - Use Caution

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 YHUANG43@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-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/1Lkhouh8JcGIBaS6fLV9JQgz1EYX4KBNrE3cpzFIcNrPR1a... 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/1q9Cla45g1qyO1JhEIHLbeCV_WzIZr41lZq5PyYZAFuCSX0... 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/1X63vCOe_tHENJcMzHMja3e-1NPoKlrHdwrPoHmnOSp_46d... < https://secure-web.cisco.com/1X63vCOe_tHENJcMzHMja3e-1NPoKlrHdwrPoHmnOSp_46d... .

External Email - Use Caution

recon-all died immediately after trying to create a symlink. Might be because it is on a VBox. Rob, can you help figure this out?

On 6/21/2023 11:55 AM, Varun Chandran 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 varunchandran28@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
<YHUANG43@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-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/1w_ORaTedKhggbpkzXnTt-_hKF9lVZNj05XdrO3033r3fOgPAbzmPKNO7j-fkZIDz7sTI3O-Z-gEfcy_s-RaDRGfkTUIIuCUmjStzeCEn0JlsO3COfjmz6ADpt4UsXI2u36Wxsgttwov_wsOgJxa4zY7U1jwLQT9CwYP8PJhhKYJOtrZNi9ri-ClsznccIXLzv8_fIw4uuD1pIj4w1jsdYDllasa7OsImc9bjuL1H3lEIgwaGmGpd1oQJF6xU0XFr/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
    *MailScanner has detected a possible fraud attempt from
    "secure-web.cisco.com" claiming to be*
    https://secure-web.cisco.com/1zR5HTLuenwZa7rEGkARJwaUsrwYbbbZcarDgxMggEvUy0An0sNk9n6hL0O20R0GgFTxOeE5B0MdsGZ3d10v8-jlUbf2bsSmMJ66ACS_ZipuhCO9T9wF7oYI4Tpxe5M4njMAXaLKNarO_RpnURuhwSvVNLbBeOilWo8H1CHqSmZjuq5V0YDLNFYSApmLRq-zvrKSg2EJORklQB2m2SS5yJYdVNl8VTqaxX2AwSDwartqLTCI5bT_RBl2sEWz504lC/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
    <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
    *MailScanner has detected a possible fraud attempt from
    "secure-web.cisco.com" claiming to be*
    https://secure-web.cisco.com/1Dsy8sqnGkW25kKE-qWpGYwRcSIkj_Kl5vDZQazqc158vMjW_gQVP5ckjEO3CMho-wMLKtiw9CAFiBKl0eMRhABGZjq8X4Xbr8EffK58JlFmXkqXzfofr-pDfc9um7zi3i4pjQ_S-896pb0ACXIl-qBTLKC-xjDbVnuBGUyEY0m_G00Mxxwp-ZpzT0zP9WUG1sCzQp_nbWMAY-RgiDDuFXrZhghketizoY5cAW_yqQxzDNgBYVBPSrR5bXhwSRk-9/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>
    <*MailScanner has detected a possible fraud attempt from
    "secure-web.cisco.com" claiming to be*
    https://secure-web.cisco.com/1Dsy8sqnGkW25kKE-qWpGYwRcSIkj_Kl5vDZQazqc158vMjW_gQVP5ckjEO3CMho-wMLKtiw9CAFiBKl0eMRhABGZjq8X4Xbr8EffK58JlFmXkqXzfofr-pDfc9um7zi3i4pjQ_S-896pb0ACXIl-qBTLKC-xjDbVnuBGUyEY0m_G00Mxxwp-ZpzT0zP9WUG1sCzQp_nbWMAY-RgiDDuFXrZhghketizoY5cAW_yqQxzDNgBYVBPSrR5bXhwSRk-9/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.

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://secure-web.cisco.com/1w_ORaTedKhggbpkzXnTt-_hKF9lVZNj05XdrO3033r3fOgPAbzmPKNO7j-fkZIDz7sTI3O-Z-gEfcy_s-RaDRGfkTUIIuCUmjStzeCEn0JlsO3COfjmz6ADpt4UsXI2u36Wxsgttwov_wsOgJxa4zY7U1jwLQT9CwYP8PJhhKYJOtrZNi9ri-ClsznccIXLzv8_fIw4uuD1pIj4w1jsdYDllasa7OsImc9bjuL1H3lEIgwaGmGpd1oQJF6xU0XFr/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fvarun-chandran-phd-49a6b258%2F
<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.

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1w_ORaTedKhggbpkzXnTt-_hKF9lVZNj05XdrO3033r3fOg... 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1zR5HTLuenwZa7rEGkARJwaUsrwYbbbZcarDgxMggEvUy0A...