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 <nayanw...@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 $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> type sh
> after sourcing and then try running it(without closing the terminal)
> hopefully, it will work that way.
>
> Thanks and Regards
> Nayan Wadhwani
>
>
> On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo <
> rdacos...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> I did it:
>>
>> # FREESURFER
>> export FREESURFER_HOME=/usr/local/freesurfer
>> export PATH=${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 <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/1OqhJyJ813mAOOYqZfdSZIa_0JPvaaP8OAG_-2fX4nN8Wl4_Hgd4jpfWwRcrPGzhIehBjjs4yOxRTb5TuyZP3LEWvB5uIqJ-Wt-TJCykYjHOZXX3Sw09hwaYyUA__5soQiMn-ZB5bBfDMNju1J8HvtOfIRT3eYwS2YzKktY83JqrYZlB4RArJYKHwf4vFHIdgD9P0hT32n-xlSD42zZvafAZvMk9bxWHBvQ9_Ul58dmhw4Fpj8DKDTpxts3Dqi8yjSsv0pX7LcVIQJOd-wNkMOA/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/1er7WkcMo1MDUucGdiReEcgSLUf4VbsBK7GsAmPijINrMjJ8LPiraEGFUoW38A6v2I3UXx03tEmKe0M4UIt5VCFcHkPCNEiYErCl3BcqI0y6k7-KM45S8dTkDi7gH0v5sNw_LifGSNo0MsAfydxcCgdPCUiHQBrpGO05WHLI0s3cW0LV5O484lhkuchjbr8nC9oKwQd_G4cHZsszH4bk_BBdBpYpXkvX3T6y4d4j6TpezwK-R_i8RBUfiNRldwbqy4ILGUFmSSuvXYMfRmmgk9g/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/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK281SbvHaGdpDyKm2QRoo1k0J9BqwlbXeVG_etB7nbbV4GglUJ1_z21Ly2rIIteMaJ-dbgDk_Wxr-WicEJEYPyWh9rARtwoNBjUgL5GjwNYWemHI57Xu1qNwFFHVQRRmvlTIWfaIwtSgtXzdyh51DGMfNYaMaHAIgtqUItyXGU8PzN-KUoPk-nmGiSEclNIaGNjfDMdipXq83_o-6uh171zYwTP5LTogyCqThczZDA/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/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK281SbvHaGdpDyKm2QRoo1k0J9BqwlbXeVG_etB7nbbV4GglUJ1_z21Ly2rIIteMaJ-dbgDk_Wxr-WicEJEYPyWh9rARtwoNBjUgL5GjwNYWemHI57Xu1qNwFFHVQRRmvlTIWfaIwtSgtXzdyh51DGMfNYaMaHAIgtqUItyXGU8PzN-KUoPk-nmGiSEclNIaGNjfDMdipXq83_o-6uh171zYwTP5LTogyCqThczZDA/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/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK281SbvHaGdpDyKm2QRoo1k0J9BqwlbXeVG_etB7nbbV4GglUJ1_z21Ly2rIIteMaJ-dbgDk_Wxr-WicEJEYPyWh9rARtwoNBjUgL5GjwNYWemHI57Xu1qNwFFHVQRRmvlTIWfaIwtSgtXzdyh51DGMfNYaMaHAIgtqUItyXGU8PzN-KUoPk-nmGiSEclNIaGNjfDMdipXq83_o-6uh171zYwTP5LTogyCqThczZDA/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
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> 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
>>> <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/17IbFKTkauAks0E4MVYeN6uIdlLHJ9wQRAogXBvuPvtRvK281SbvHaGdpDyKm2QRoo1k0J9BqwlbXeVG_etB7nbbV4GglUJ1_z21Ly2rIIteMaJ-dbgDk_Wxr-WicEJEYPyWh9rARtwoNBjUgL5GjwNYWemHI57Xu1qNwFFHVQRRmvlTIWfaIwtSgtXzdyh51DGMfNYaMaHAIgtqUItyXGU8PzN-KUoPk-nmGiSEclNIaGNjfDMdipXq83_o-6uh171zYwTP5LTogyCqThczZDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <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
> 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
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