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 <p...@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 <
> rdacos...@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/1Dkw2-i5FxQUOt9lpu4plHCwpFMgIwDAEzE9vPosQv2XySKsjDg6elpjchpQTLLb1rAFImaFaPCp5VSzcM40lY1FgvMce1nACIXP21VSWF2kA3WiM6RtiEyABkTG7_G_sTNihrrEmfBxiLArOd3hCYbWpuGzzlh41xB2rcgPiZljN9JU3GHO0296wzSPy1x1thWw-f-vk6gCsqQ2-0jhZVChxSCqvZMGCzhNZsa-QW83swplo9vFeSyEM6eSEDV_DXRBwxjMiC6oo-RS74PbI7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
>> <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 <
>> rdacos...@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-LrOVT9uxHbVqauNyWDlV1o85DW4fbAerH5zERE56QhGxvmXIqCteCuDMivfuw88IOeaXM0T0c-b6gBGVhvm3hlN_mPk1b4UY6IMgXlHMz48yk3_JkUwCHIHpFMb4L4d4-tIWCpG4wveRGNQkR5eeLpiBLW-S6HHIT3KIEiWa_-vx52KHTPxLFVDcDzw203ET5ETMTmHkIY6yGvF4GNszxYva-G20DKxbjMWoGjW-AGKFuXpm7jbnnqW05qE2os-HnIghlJeEf3uXLgw3hr0g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldSegmentation
>>> <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_xXJ8GcWw6Nw0yZD-cWHRtWV-JD7V865yLD_F4lYjs6EZ5FGeKzqynqi9KCnxf_clErB_-lj5rI7bLxygbb7gfQrs9Gdr4-KFGNiNEoPwuEkOGm-BOA3gGuhEyJ572DCFCCywpW3fwdjKbSGLiq1Q8CwRoa43viygIsONuIeiTmD2e_SXax5cFFwjpCkds9Efsnb8Eb7k5VAomcjoc-m6zILmfRnpFqJEfTUScU5Xg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <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_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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