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 <p...@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 <
> 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/1-8yalAFoH2d-PHWhHyM5iEfm3KBqAB6ae0473lww8lW4utKuFxt-ZFjzmepn934o_QxivTXyv6JNO0mRsxJlT35w8NZ7LGBWi9V-XAIJeIR6r3URKVNKpcueF2v0Sk8OcsvcB7AGEtckFWzodDa4gROTHTK6Y2zmj_CoObXSsGjqfFUIGSyl7p0OtY_GVcq_nD7jpg6dgiuNJMWQifywMeCwdbqqFj32mEfV3JKSdmtgttX3AwpKHVZn_6imDEf3CNRa4r3z4BaUCYqESpRsiA/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/11AMJvdn1j2hxYKns2TyK0jt4b0JcG9kyw8we64JEQtemnvLPwFAW1Kg4X0FfxxD5FqL359mghH_x-0kAV3E_K1h2JJiUs9YE2FTdFiw9hwzy3oe4sG4hK9918H5pOq2o0XVS5sUdwRDAoUrb5_3kxdfOuP6NRo3FVji2UNBAyTNV5kGMlW3jr-mOgI2aSxytMeGVkIKFdrV04Tno8VHDxqWagcKF84YO_e91KLnCH4NE7qyV7mLFRvcco24Ws4OdddMhrAQe8WknVSrlyoKVaQ/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/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/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/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/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
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1b4G_oXHixX2N6JxpyTXp3Ua7FQF69m4PCdd_YrnXwM4Y25SSxBKEBohag1BIo61F3KhVPMk1fSfWOkSa9EHeGZ7KC_3ltadxQwAFWG_emHkqA4RJ507RJo3hpf858suO7Xof4snvNXHmEbEoZt-Z3mqr333m9XVbvtTRyd7hGEHCcpi9H59z7R0Rqx_XXvA1FsjohAWrzU_626pD9idupiXIwuxeqvHC7rkFrgaOHpiOUZvqa0q7yX23RmFRuvBL0TZovZulUuyVozRWPjzf9Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <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
> 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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