External Email - Use Caution
Dear Freesurfer team,
Following this link: https://secure-web.cisco.com/1JQvIqqm3-q4IvkVi2SEZWuHP3qoo3qga0SfN71vLNIZ9qj...
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
External Email - Use Caution
Following this more actualized link: https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0Q...
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
Dear Freesurfer team,
Following this link: https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGU...
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
External Email - Use Caution
Hi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xJ_x-nVoRHJ_8tlPreFyUXBI47cl6teOQogPB6cqAAZMZs... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
Dear Freesurfer team,
Following this link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1OH9tdDUm2xb0DBlFPNf9MCt5qwMcva-qL58p29JrWNboyX... https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7...
External Email - Use Caution
Hi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Dkw2-i5FxQUOt9lpu4plHCwpFMgIwDAEzE9vPosQv2XySK... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
Dear Freesurfer team,
Following this link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1p-LrOVT9uxHbVqauNyWDlV1o85DW4fbAerH5zERE56QhGx... https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
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/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_x... https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_x...
External Email - Use Caution
Sure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/12pNhwbezvqVOnWuucJ4jnVcXXeYEXVyu7dJoNkrgyPy5ia... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
Dear Freesurfer team,
Following this link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-RiYxu5iLuhI6RgTSsaLtmUd6KKPV1Rrcr6Q0I55hoECKX... https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
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/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpe... https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpe... https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpe...
External Email - Use Caution
Hi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-8yalAFoH2d-PHWhHyM5iEfm3KBqAB6ae0473lww8lW4ut... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
Dear Freesurfer team,
Following this link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/11AMJvdn1j2hxYKns2TyK0jt4b0JcG9kyw8we64JEQtemnv... https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
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/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25... https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Dear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1GkrlAYjqlnbk3q7VX5LLmcVI9cUDcfMnFG1fucd4TA6hgS... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
Dear Freesurfer team,
Following this link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/10sqb1n1jGOzAGOp6CyM7XBr18SydqsBY5vjjg7mlweYDJ8... https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run.
Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated.
Kind regards, Rosie
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/1OBblZOUAbZ0LM80VTg1lNPjwERt9ko5uYc9GNV9Ta9Sjjq... https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Hi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1OqhJyJ813mAOOYqZfdSZIa_0JPvaaP8OAG_-2fX4nN8Wl4... https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
When I run the command, it gives me this error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh sub-002_ses-BSL segmentHA_T1.sh: command not found rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $
Any idea what I am doing wrong?
Kind regards, Rosie
On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
> Dear Freesurfer team, > > Following this link: *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1er7WkcMo1MDUucGdiReEcgSLUf4VbsBK7GsAmPijINrMjJ... > https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation > > It says how to run segmentation of hippocampal subfields before > running recon-all but not once you already have recon-all -all run. > > Any suggestions on how I can get the segmentation of hippocampal > subfields under this situation would be appreciated. > > Kind regards, > Rosie > > > _______________________________________________ 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/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK2... https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Ok, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionHi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin directory. It looks like your PATH environment variable does not include this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo $FREESURFER_HOME`), you should be able to update your PATH with `export PATH=${FREESURFER_HOME}/bin:${PATH}`**
Commands to set FREESURFER_HOME and update your PATH can be added to your shell startup script (e.g. ~/.bashrc) so they are executed automatically when you open a shell window.
** This assumes your shell is bash. The commands may be slightly different if using a different shell.
-Paul
On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
> External Email - Use Caution > > Following this more actualized link: *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1QkqmryHlmSo2BLsXA4nDfN2RPHoO3L1I9knuOQHCp57aga... > https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala > > When I run the command, it gives me this error: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ > segmentHA_T1.sh sub-002_ses-BSL > segmentHA_T1.sh: command not found > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ > > > Any idea what I am doing wrong? > > Kind regards, > Rosie > > > On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < > rdacostaa@gmail.com> wrote: > >> Dear Freesurfer team, >> >> Following this link: *MailScanner has detected a possible fraud >> attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1f185UoB5-sGRguH6ElRIoLW9b1uzReuYC4OWDvN8z3gj_t... >> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >> >> It says how to run segmentation of hippocampal subfields before >> running recon-all but not once you already have recon-all -all run. >> >> Any suggestions on how I can get the segmentation of hippocampal >> subfields under this situation would be appreciated. >> >> Kind regards, >> Rosie >> >> >> _______________________________________________ > 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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... > https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH...
External Email - Use Caution
Here it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
Thank you very much for answering my question. I set the subjects_dir in a way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME /usr/local/freesurfer rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
I would greatly appreciate it if you could be more specific with my example as I am new on this and I am a bit lost.
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com wrote:
> External Email - Use Caution > > Hi Rosie, > > The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin > directory. It looks like your PATH environment variable does not > include this directory. > > If the $FREESURFER_HOME variable is set (you can check by running > `echo $FREESURFER_HOME`), you should be able to update your PATH with > `export PATH=${FREESURFER_HOME}/bin:${PATH}`** > > Commands to set FREESURFER_HOME and update your PATH can be added to > your shell startup script (e.g. ~/.bashrc) so they are executed > automatically when you open a shell window. > > ** This assumes your shell is bash. The commands may be > slightly different if using a different shell. > > -Paul > > On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < > rdacostaa@gmail.com> wrote: > >> External Email - Use Caution >> >> Following this more actualized link: *MailScanner has detected a >> possible fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1DdMUK3S4zYzIDWd8UtI5oeoWvWllyVLkFvm55vdbSnX3-f... >> https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala >> >> When I run the command, it gives me this error: >> >> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >> segmentHA_T1.sh sub-002_ses-BSL >> segmentHA_T1.sh: command not found >> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >> >> >> Any idea what I am doing wrong? >> >> Kind regards, >> Rosie >> >> >> On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < >> rdacostaa@gmail.com> wrote: >> >>> Dear Freesurfer team, >>> >>> Following this link: *MailScanner has detected a possible fraud >>> attempt from "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/15ys_jrUcv61484Q8FCDy-vbGTtx5Hmgx5Lc_PuSa6iMiku... >>> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >>> >>> It says how to run segmentation of hippocampal subfields before >>> running recon-all but not once you already have recon-all -all run. >>> >>> Any suggestions on how I can get the segmentation of hippocampal >>> subfields under this situation would be appreciated. >>> >>> Kind regards, >>> Rosie >>> >>> >>> _______________________________________________ >> 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/1ELBMS2cXksyrT2cBRrEpaPmjkIyYqSU51cQU7y3ubO2cMV... >> https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > 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/1ELBMS2cXksyrT2cBRrEpaPmjkIyYqSU51cQU7y3ubO2cMV... > https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Thanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version.
There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: https://secure-web.cisco.com/1yG2oNYO-Rk8MmvOxXyxAXK4xUf0I1w4DLd-6h6jEgglbga...
Otherwise, if you upgrade to the latest version (v7.1.1) you can use the segmentHA_T1.sh script.
-Paul
On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHere it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionSure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows, open a new one and try running `segmentHA_T1.sh` again.
-Paul
On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
> External Email - Use Caution > > Hi Paul, > > Thank you very much for answering my question. I set the > subjects_dir in a way I can run freesufer in CAN_RUTI folder. > > When I do what you ask me to do: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME > /usr/local/freesurfer > rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc > rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ > > > # FREESURFER > export FREESURFER_HOME=/usr/local/freesurfer > export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > I would greatly appreciate it if you could be more specific with my > example as I am new on this and I am a bit lost. > > Kind regards, > Rosie > > > > > > > > On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton paul@corticometrics.com > wrote: > >> External Email - Use Caution >> >> Hi Rosie, >> >> The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin >> directory. It looks like your PATH environment variable does not >> include this directory. >> >> If the $FREESURFER_HOME variable is set (you can check by running >> `echo $FREESURFER_HOME`), you should be able to update your PATH with >> `export PATH=${FREESURFER_HOME}/bin:${PATH}`** >> >> Commands to set FREESURFER_HOME and update your PATH can be added >> to your shell startup script (e.g. ~/.bashrc) so they are executed >> automatically when you open a shell window. >> >> ** This assumes your shell is bash. The commands may be >> slightly different if using a different shell. >> >> -Paul >> >> On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < >> rdacostaa@gmail.com> wrote: >> >>> External Email - Use Caution >>> >>> Following this more actualized link: *MailScanner has detected a >>> possible fraud attempt from "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1gdObUDkVw3BzMd52yPaj9aERew5JMGzwOu6Ag7mcytT0hh... >>> https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala >>> >>> When I run the command, it gives me this error: >>> >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>> segmentHA_T1.sh sub-002_ses-BSL >>> segmentHA_T1.sh: command not found >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>> >>> >>> Any idea what I am doing wrong? >>> >>> Kind regards, >>> Rosie >>> >>> >>> On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < >>> rdacostaa@gmail.com> wrote: >>> >>>> Dear Freesurfer team, >>>> >>>> Following this link: *MailScanner has detected a possible fraud >>>> attempt from "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1HG83QKYf61_Nov899f2pxZT0250zS_FmUD8RqyC3Pjgj07... >>>> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >>>> >>>> It says how to run segmentation of hippocampal subfields before >>>> running recon-all but not once you already have recon-all -all run. >>>> >>>> Any suggestions on how I can get the segmentation of hippocampal >>>> subfields under this situation would be appreciated. >>>> >>>> Kind regards, >>>> Rosie >>>> >>>> >>>> _______________________________________________ >>> 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/11CF8irkEjFgKt5cvXvvk4KyAyvcAwDxBoKxplMUbScfXRZ... >>> https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> _______________________________________________ >> 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/11CF8irkEjFgKt5cvXvvk4KyAyvcAwDxBoKxplMUbScfXRZ... >> https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > 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/11CF8irkEjFgKt5cvXvvk4KyAyvcAwDxBoKxplMUbScfXRZ... > https://secure-web.cisco.com/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Hi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I made some corrections (control points,...). I just want the hipocampal subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionThanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version.
There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1fl8L9dCCiXj5DJ5VqsSKSwM9wVLC6JVbFZlf1dNkmWN2IT... https://secure-web.cisco.com/1yG2oNYO-Rk8MmvOxXyxAXK4xUf0I1w4DLd-6h6jEgglbgaEu_bTXvX6ZZCH-CJjPD9OFaIQLCe3ifyaJhyDl1D0zzu2FxEKkYiL7ORLQBuGkPlxhMHNO_fjTLguHjY0470nArGjzSNK_okSRQR36E06HStZjHAzrPyNFRofrqANGoW0OlMSFsJRiFZkqOOetHjGUx45LipBooxBUq1N2m679dT0cWGbgNBd3ZGMfbd90aICTFZQ8KoXaWy7vcgXaDW6e3vulDZ9jrSwFH8ifZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields
Otherwise, if you upgrade to the latest version (v7.1.1) you can use the segmentHA_T1.sh script.
-Paul
On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHere it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${FREESURFER_HOME}/bin:${PATH} export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer but it does not seem to recognize the command: rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh segmentHA_T1.sh: command not found
Kind regards, Rosie
On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com wrote:
> External Email - Use Caution > > Sure Rosie, no worries. > > Try adding the following line to the end of your ~/.bashrc (it must > come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'): > > export PATH=${FREESURFER_HOME}/bin:${PATH} > > After saving, close all your terminal windows, open a new one and > try running `segmentHA_T1.sh` again. > > -Paul > > > On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < > rdacostaa@gmail.com> wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> Thank you very much for answering my question. I set the >> subjects_dir in a way I can run freesufer in CAN_RUTI folder. >> >> When I do what you ask me to do: >> >> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME >> /usr/local/freesurfer >> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc >> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ >> >> >> # FREESURFER >> export FREESURFER_HOME=/usr/local/freesurfer >> export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> I would greatly appreciate it if you could be more specific with my >> example as I am new on this and I am a bit lost. >> >> Kind regards, >> Rosie >> >> >> >> >> >> >> >> On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton < >> paul@corticometrics.com> wrote: >> >>> External Email - Use Caution >>> >>> Hi Rosie, >>> >>> The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin >>> directory. It looks like your PATH environment variable does not >>> include this directory. >>> >>> If the $FREESURFER_HOME variable is set (you can check by running >>> `echo $FREESURFER_HOME`), you should be able to update your PATH with >>> `export PATH=${FREESURFER_HOME}/bin:${PATH}`** >>> >>> Commands to set FREESURFER_HOME and update your PATH can be added >>> to your shell startup script (e.g. ~/.bashrc) so they are executed >>> automatically when you open a shell window. >>> >>> ** This assumes your shell is bash. The commands may be >>> slightly different if using a different shell. >>> >>> -Paul >>> >>> On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < >>> rdacostaa@gmail.com> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Following this more actualized link: *MailScanner has detected a >>>> possible fraud attempt from "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/10-cnJEcvF0EznNdkvF4bWb5YPofYYfkG6S9A_5M6kxFOKD... >>>> https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala >>>> >>>> When I run the command, it gives me this error: >>>> >>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>> segmentHA_T1.sh sub-002_ses-BSL >>>> segmentHA_T1.sh: command not found >>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>> >>>> >>>> Any idea what I am doing wrong? >>>> >>>> Kind regards, >>>> Rosie >>>> >>>> >>>> On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < >>>> rdacostaa@gmail.com> wrote: >>>> >>>>> Dear Freesurfer team, >>>>> >>>>> Following this link: *MailScanner has detected a possible fraud >>>>> attempt from "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1zUDzhpjTUy1Nd7mgSl4BSH-m6mxZ7s9A00xLfr4e1pG6nE... >>>>> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >>>>> >>>>> It says how to run segmentation of hippocampal subfields before >>>>> running recon-all but not once you already have recon-all -all run. >>>>> >>>>> Any suggestions on how I can get the segmentation of hippocampal >>>>> subfields under this situation would be appreciated. >>>>> >>>>> Kind regards, >>>>> Rosie >>>>> >>>>> >>>>> _______________________________________________ >>>> 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/1JgEqf8LbjrLIYmL-h8qP8Jr_n7Y-SlrHvjb50pupkEdYKA... >>>> https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> _______________________________________________ >>> 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/1JgEqf8LbjrLIYmL-h8qP8Jr_n7Y-SlrHvjb50pupkEdYKA... >>> https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> _______________________________________________ >> 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/1JgEqf8LbjrLIYmL-h8qP8Jr_n7Y-SlrHvjb50pupkEdYKA... >> https://secure-web.cisco.com/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > 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/1JgEqf8LbjrLIYmL-h8qP8Jr_n7Y-SlrHvjb50pupkEdYKA... > https://secure-web.cisco.com/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Hi Rosie,
In that case, you can try running the v6 version of hippocampal subfields, e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I made some corrections (control points,...). I just want the hipocampal subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionThanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version.
There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1t2_b4MKmj7AoD1ilytwc27ttmNirqEgD9Kp2gLIS9JfUW5... https://secure-web.cisco.com/1yG2oNYO-Rk8MmvOxXyxAXK4xUf0I1w4DLd-6h6jEgglbgaEu_bTXvX6ZZCH-CJjPD9OFaIQLCe3ifyaJhyDl1D0zzu2FxEKkYiL7ORLQBuGkPlxhMHNO_fjTLguHjY0470nArGjzSNK_okSRQR36E06HStZjHAzrPyNFRofrqANGoW0OlMSFsJRiFZkqOOetHjGUx45LipBooxBUq1N2m679dT0cWGbgNBd3ZGMfbd90aICTFZQ8KoXaWy7vcgXaDW6e3vulDZ9jrSwFH8ifZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields
Otherwise, if you upgrade to the latest version (v7.1.1) you can use the segmentHA_T1.sh script.
-Paul
On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHere it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
> External Email - Use Caution > > Hi Paul, > > I did it: > > # FREESURFER > export FREESURFER_HOME=/usr/local/freesurfer > export PATH=${FREESURFER_HOME}/bin:${PATH} > export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > And I even re-started the computer but it does not seem to recognize > the command: > rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh > segmentHA_T1.sh: command not found > > Kind regards, > Rosie > > > > > On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton paul@corticometrics.com > wrote: > >> External Email - Use Caution >> >> Sure Rosie, no worries. >> >> Try adding the following line to the end of your ~/.bashrc (it must >> come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'): >> >> export PATH=${FREESURFER_HOME}/bin:${PATH} >> >> After saving, close all your terminal windows, open a new one and >> try running `segmentHA_T1.sh` again. >> >> -Paul >> >> >> On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < >> rdacostaa@gmail.com> wrote: >> >>> External Email - Use Caution >>> >>> Hi Paul, >>> >>> Thank you very much for answering my question. I set the >>> subjects_dir in a way I can run freesufer in CAN_RUTI folder. >>> >>> When I do what you ask me to do: >>> >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME >>> /usr/local/freesurfer >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc >>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ >>> >>> >>> # FREESURFER >>> export FREESURFER_HOME=/usr/local/freesurfer >>> export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI >>> source $FREESURFER_HOME/SetUpFreeSurfer.sh >>> >>> I would greatly appreciate it if you could be more specific with >>> my example as I am new on this and I am a bit lost. >>> >>> Kind regards, >>> Rosie >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton < >>> paul@corticometrics.com> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Hi Rosie, >>>> >>>> The segmentHA_T1.sh script is located in the >>>> $FREESURFER_HOME/bin directory. It looks like your PATH environment >>>> variable does not include this directory. >>>> >>>> If the $FREESURFER_HOME variable is set (you can check by running >>>> `echo $FREESURFER_HOME`), you should be able to update your PATH with >>>> `export PATH=${FREESURFER_HOME}/bin:${PATH}`** >>>> >>>> Commands to set FREESURFER_HOME and update your PATH can be added >>>> to your shell startup script (e.g. ~/.bashrc) so they are executed >>>> automatically when you open a shell window. >>>> >>>> ** This assumes your shell is bash. The commands may be >>>> slightly different if using a different shell. >>>> >>>> -Paul >>>> >>>> On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < >>>> rdacostaa@gmail.com> wrote: >>>> >>>>> External Email - Use Caution >>>>> >>>>> Following this more actualized link: *MailScanner has detected >>>>> a possible fraud attempt from "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1qtepMLmh0ZkJ9Lm-1L5p9PE5z4LDSTgmsbtE328kTZyR0W... >>>>> https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala >>>>> >>>>> When I run the command, it gives me this error: >>>>> >>>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>>> segmentHA_T1.sh sub-002_ses-BSL >>>>> segmentHA_T1.sh: command not found >>>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>>> >>>>> >>>>> Any idea what I am doing wrong? >>>>> >>>>> Kind regards, >>>>> Rosie >>>>> >>>>> >>>>> On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < >>>>> rdacostaa@gmail.com> wrote: >>>>> >>>>>> Dear Freesurfer team, >>>>>> >>>>>> Following this link: *MailScanner has detected a possible >>>>>> fraud attempt from "secure-web.cisco.com" claiming to be* >>>>>> https://secure-web.cisco.com/1o4b9ojP3xIAU6boGSdAet5MVdgyFqLwWz7wdrqEGy9XbfJ... >>>>>> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >>>>>> >>>>>> It says how to run segmentation of hippocampal subfields before >>>>>> running recon-all but not once you already have recon-all -all run. >>>>>> >>>>>> Any suggestions on how I can get the segmentation of >>>>>> hippocampal subfields under this situation would be appreciated. >>>>>> >>>>>> Kind regards, >>>>>> Rosie >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>> 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/1mzvnhrk2Yqq6KlT1qVFnWUxygDJ7ezZ74dWRo0KqWe7fuo... >>>>> https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> _______________________________________________ >>>> 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/1mzvnhrk2Yqq6KlT1qVFnWUxygDJ7ezZ74dWRo0KqWe7fuo... >>>> https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> _______________________________________________ >>> 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/1mzvnhrk2Yqq6KlT1qVFnWUxygDJ7ezZ74dWRo0KqWe7fuo... >>> https://secure-web.cisco.com/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> _______________________________________________ >> 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/1mzvnhrk2Yqq6KlT1qVFnWUxygDJ7ezZ74dWRo0KqWe7fuo... >> https://secure-web.cisco.com/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > 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/1mzvnhrk2Yqq6KlT1qVFnWUxygDJ7ezZ74dWRo0KqWe7fuo... > https://secure-web.cisco.com/1OBblZOUAbZ0LM80VTg1lNPjwERt9ko5uYc9GNV9Ta9SjjqGl6VTCIjA1Fs1GvqO5viXO331CIfoaVhJJovyZgMd6Wh-XbKc_QzY8tHfuTAT_EK710kK92JEZ4Dng5Yr_evUWjm4HHZMHKIkgDwdXwebgsLn-NyASOhFaj3tzXFYsVd2T4yXVA2rW75GVzdZWpbVS5sq9jTV6TJVEBgQGsLOhQ-gx339QnMFJ4pxaZMeQ4qPAOHh9zhCL_2fehuOby9i-v4lS3GeApjx8V2BIqw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
Thanks!!!
Kind regards, Rosie
El mié., 7 jul. 2021 21:32, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionHi Rosie,
In that case, you can try running the v6 version of hippocampal subfields, e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I made some corrections (control points,...). I just want the hipocampal subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionThanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version.
There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1rLyfwTNMrD8uPGQPvaKYcfc7uDe6gWOoA1V_iVTwU9RHJm... https://secure-web.cisco.com/1yG2oNYO-Rk8MmvOxXyxAXK4xUf0I1w4DLd-6h6jEgglbgaEu_bTXvX6ZZCH-CJjPD9OFaIQLCe3ifyaJhyDl1D0zzu2FxEKkYiL7ORLQBuGkPlxhMHNO_fjTLguHjY0470nArGjzSNK_okSRQR36E06HStZjHAzrPyNFRofrqANGoW0OlMSFsJRiFZkqOOetHjGUx45LipBooxBUq1N2m679dT0cWGbgNBd3ZGMfbd90aICTFZQ8KoXaWy7vcgXaDW6e3vulDZ9jrSwFH8ifZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields
Otherwise, if you upgrade to the latest version (v7.1.1) you can use the segmentHA_T1.sh script.
-Paul
On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHere it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory
What version of FreeSurfer is installed at /usr/local/freesurfer? Can you run the following command and copy the output
cat $FREESURFER_HOME/build-stamp.txt
-Paul
On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh $ segmentHA_T1.sh sh: 1: segmentHA_T1.sh: not found $
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani nayanw775@gmail.com wrote:
> External Email - Use Caution > > Dear Rosalia, > > Once you export and source freesurfer with the following commands > > export FREESURFER_HOME=/usr/local/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > type sh > after sourcing and then try running it(without closing the > terminal) hopefully, it will work that way. > > Thanks and Regards > Nayan Wadhwani > > > On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < > rdacostaa@gmail.com> wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> I did it: >> >> # FREESURFER >> export FREESURFER_HOME=/usr/local/freesurfer >> export PATH=${FREESURFER_HOME}/bin:${PATH} >> export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> And I even re-started the computer but it does not seem to >> recognize the command: >> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ segmentHA_T1.sh >> segmentHA_T1.sh: command not found >> >> Kind regards, >> Rosie >> >> >> >> >> On Wed, Jul 7, 2021 at 6:47 PM Paul Wighton < >> paul@corticometrics.com> wrote: >> >>> External Email - Use Caution >>> >>> Sure Rosie, no worries. >>> >>> Try adding the following line to the end of your ~/.bashrc (it >>> must come after the line 'export FREESURFER_HOME=/usr/local/freesurfer'): >>> >>> export PATH=${FREESURFER_HOME}/bin:${PATH} >>> >>> After saving, close all your terminal windows, open a new one and >>> try running `segmentHA_T1.sh` again. >>> >>> -Paul >>> >>> >>> On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < >>> rdacostaa@gmail.com> wrote: >>> >>>> External Email - Use Caution >>>> >>>> Hi Paul, >>>> >>>> Thank you very much for answering my question. I set the >>>> subjects_dir in a way I can run freesufer in CAN_RUTI folder. >>>> >>>> When I do what you ask me to do: >>>> >>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME >>>> /usr/local/freesurfer >>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ gedit ~/.bashrc >>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ >>>> >>>> >>>> # FREESURFER >>>> export FREESURFER_HOME=/usr/local/freesurfer >>>> export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI >>>> source $FREESURFER_HOME/SetUpFreeSurfer.sh >>>> >>>> I would greatly appreciate it if you could be more specific with >>>> my example as I am new on this and I am a bit lost. >>>> >>>> Kind regards, >>>> Rosie >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Wed, Jul 7, 2021 at 6:32 PM Paul Wighton < >>>> paul@corticometrics.com> wrote: >>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi Rosie, >>>>> >>>>> The segmentHA_T1.sh script is located in the >>>>> $FREESURFER_HOME/bin directory. It looks like your PATH environment >>>>> variable does not include this directory. >>>>> >>>>> If the $FREESURFER_HOME variable is set (you can check by >>>>> running `echo $FREESURFER_HOME`), you should be able to update your PATH >>>>> with `export PATH=${FREESURFER_HOME}/bin:${PATH}`** >>>>> >>>>> Commands to set FREESURFER_HOME and update your PATH can be >>>>> added to your shell startup script (e.g. ~/.bashrc) so they are executed >>>>> automatically when you open a shell window. >>>>> >>>>> ** This assumes your shell is bash. The commands may be >>>>> slightly different if using a different shell. >>>>> >>>>> -Paul >>>>> >>>>> On Tue, Jul 6, 2021 at 11:42 AM Rosalia Dacosta Aguayo < >>>>> rdacostaa@gmail.com> wrote: >>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Following this more actualized link: *MailScanner has detected >>>>>> a possible fraud attempt from "secure-web.cisco.com" claiming to be* >>>>>> https://secure-web.cisco.com/1UOXPN9Y_Lpnff1I-uWNXLM-VvbTewnSXhiAnzvlaEJ3DKS... >>>>>> https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoTxXXQUDaufWAGWvcAVqiwBXQtF106QHM6fplsqgPemPccDFDES4yyFJmuWU70g7FR5w6f_0M7Jr1hcS41Qt3TOypkKOPw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala >>>>>> >>>>>> When I run the command, it gives me this error: >>>>>> >>>>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>>>> segmentHA_T1.sh sub-002_ses-BSL >>>>>> segmentHA_T1.sh: command not found >>>>>> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >>>>>> >>>>>> >>>>>> Any idea what I am doing wrong? >>>>>> >>>>>> Kind regards, >>>>>> Rosie >>>>>> >>>>>> >>>>>> On Tue, Jul 6, 2021 at 5:32 PM Rosalia Dacosta Aguayo < >>>>>> rdacostaa@gmail.com> wrote: >>>>>> >>>>>>> Dear Freesurfer team, >>>>>>> >>>>>>> Following this link: *MailScanner has detected a possible >>>>>>> fraud attempt from "secure-web.cisco.com" claiming to be* >>>>>>> https://secure-web.cisco.com/1O-IsozxKzMa7OW1F4vkS4Gq--QMEHhSpc2SRUgUumNKUxZ... >>>>>>> https://secure-web.cisco.com/1fQCWx6VvVe6bnQBSadUABOYFVbWEBpT0ywgDNDDsVpzEGUBH_kg2PkoWx0F3kwRGJVaDxNSJwkHTwqevqOZSGZ8ULz_R7OboB9M1Ba0V1nC1be99hx6HywXYKaK72JzFzDxxlZeEoFsLiXoO5YJEbvJr6o3NF64CxbWe3UBYkT2ppGaaa8wlHYbRMUZdARuEu56utqfXKJd12ikiPqxTF5W7HYKJUAQyGmzCaldBNmYbavAHh9lZ-8_hKAPYmRVw-W3qiZ84ei0nzJ_8tPXlhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation >>>>>>> >>>>>>> It says how to run segmentation of hippocampal subfields >>>>>>> before running recon-all but not once you already have recon-all -all run. >>>>>>> >>>>>>> Any suggestions on how I can get the segmentation of >>>>>>> hippocampal subfields under this situation would be appreciated. >>>>>>> >>>>>>> Kind regards, >>>>>>> Rosie >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>>>> https://secure-web.cisco.com/1zyHSzZEngxMW5RxmNZeUiiItm9JF9jADXnpBS-J9zLIYY7PeJ3h0ZEm94BM9WTTAc2x4ZUvUoMU5pK4gXH7jtOc0TgPnpoZpx8eKWZnr5g12OX5eZJbO0gRhtf1iLAWcXiCeNHDmtOpeqM_jrVmHb5OcQI2yLMS_xibYDlIZ_WkKYRGv-Qf02qqa_Tbt0ZwVCcfVcVvq9uIVgpmXHinX61MZ6zAcK1hOVsL65F4OrM2b7m1-hbcZlXagT01ttCO24U2QOWo7RGlxFhGHKtU8_g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> >>>>> _______________________________________________ >>>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>>> https://secure-web.cisco.com/134cIMynbyfuW0Sqv8-0ZDNiuteZlhsNuVpf96rffbbvl_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> _______________________________________________ >>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>> https://secure-web.cisco.com/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> _______________________________________________ >>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>> https://secure-web.cisco.com/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> _______________________________________________ >> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >> https://secure-web.cisco.com/1OBblZOUAbZ0LM80VTg1lNPjwERt9ko5uYc9GNV9Ta9SjjqGl6VTCIjA1Fs1GvqO5viXO331CIfoaVhJJovyZgMd6Wh-XbKc_QzY8tHfuTAT_EK710kK92JEZ4Dng5Yr_evUWjm4HHZMHKIkgDwdXwebgsLn-NyASOhFaj3tzXFYsVd2T4yXVA2rW75GVzdZWpbVS5sq9jTV6TJVEBgQGsLOhQ-gx339QnMFJ4pxaZMeQ4qPAOHh9zhCL_2fehuOby9i-v4lS3GeApjx8V2BIqw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... > https://secure-web.cisco.com/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK281SbvHaGdpDyKm2QRoo1k0J9BqwlbXeVG_etB7nbbV4GglUJ1_z21Ly2rIIteMaJ-dbgDk_Wxr-WicEJEYPyWh9rARtwoNBjUgL5GjwNYWemHI57Xu1qNwFFHVQRRmvlTIWfaIwtSgtXzdyh51DGMfNYaMaHAIgtqUItyXGU8PzN-KUoPk-nmGiSEclNIaGNjfDMdipXq83_o-6uh171zYwTP5LTogyCqThczZDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... https://secure-web.cisco.com/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F...
freesurfer@nmr.mgh.harvard.edu
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nayan wadhwani -
Paul Wighton -
Rosalia Dacosta Aguayo