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 <rdacos...@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 <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/12pNhwbezvqVOnWuucJ4jnVcXXeYEXVyu7dJoNkrgyPy5iaNtxRJt-z5AIdyH_Uds2BaBnlmuWSY4B7osSRIU_mEGonaV9AYsuTk_uFGwcmXxARWpWcNXR1BuX3m3F_OOphsVXQaBgtKtMsyEFmR81WEZEphmvELBHPbvVInBH9I8y8mcnwWyV0HwFaHaNvyMMZ_DO9RHS3-0BsdnoB7whV7sV0nQcwRfKACXRX3tg_yiVpAC4erBvTZ2XgXbELDz3ITfBH4sxQBYtQMp7Yt5Jw/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/1-RiYxu5iLuhI6RgTSsaLtmUd6KKPV1Rrcr6Q0I55hoECKX26j_mm7GacY3297WG57-g58ul4YcoXQcfTZqXoHBXXKk-bOWk-Eel-jM5RVhrGofPd7mfx_9NKhFJ_Nd7uP9el5sMaalFLi4Rxf6apNV3qBQpuiDOOUDtQzuoY31V49ft6eOLlipV-G05PF55f1ujXhRYQdkDD6LzY5tfrY3a3NT7sTWNVW3hRb_-6xdA-LVMNLVlJtFbQ9GlvS4JeACO6-3kU1C1UwT7Mk_O_lw/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/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/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
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> 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
>> <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/1yskBCIBMHD8Hx4y9lohTJoHsr0T0Fut6W7DDOOdTG2BEpeT34cxXT69S_GMjQ4-yXxktR53GAReSMycEEqbMzP4aluwrOQtswFDxgphLe4WLit1jaWbZ_gDxVSC9tPsMK3POwsPk3w6zz8zVJxKB1CUXwC5Pag1MNF9K-cmcVObOnBElqxtyqhfK5IpMGoejAR2beL_FiXDEgUv9DAqY6yFgD-_1WcCxN829MijMtU0oxdcrjxdVNrR4DOSI4uLok_I1EunYr_Ze0LRvwwl2ew/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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