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 <rdacos...@gmail.com>
wrote:
> 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/1QkqmryHlmSo2BLsXA4nDfN2RPHoO3L1I9knuOQHCp57agaYH5sE4dh7S03DNNHfhKTW9ox1nx54N4nGdotgtBnJ37l_iM-9xgsozKfQ2d6R1cR1q_sMpzDv5tgI4IuqUrnAA_WHmZopxz72kdL2rozp82VA0cqa2O3uVdELsDYFg2-huctefKKbBNKw_VgHBCWc6RVPlDdctgL-w6zy-4zyJvFmiJmhTWm5fSME5DNCFQ-a4_JC9HFlIwIKUi75eRWTlQkVec-sjhlKikWvsLg/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/1f185UoB5-sGRguH6ElRIoLW9b1uzReuYC4OWDvN8z3gj_t0JwSqEQvFQGaHBaMtrGVSogNHx-63ey-eREPbb086jsdnaJvnWuDqffgGC-fPxARUOYEqZnVY35VXuHJ1X9O0-1ANULqvaHi8kwBF-pMA7GqXfx4P6MQ7tlpeWkMah2GRKCuiaVHtPjTikpp_cdBwlfP5fkfQ1nLzJFdi1wi1PcEpvJ-Y_R6GRTpnQhw9AYvjLG6SSvhcLGQ8xjDyctkuERvKY8Ybko2gT8EYZYg/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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/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/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/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
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <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
> https://secure-web.cisco.com/1Vm6eQ4T_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNHu-j0T5J0SVYct5yZWQtWUIHRz3lgplJdt9NMxgmHpjlPYfPQRw0ORk0PdT_Gsb6HFE6n755suN5-sU0ZTPVTBoN4vcNewm6fyl2YZ8VnfHUjlZvZBOeEUK7GytK_IywD9FhNRhbQokmC8GBSQzjs6sjkVCjy6l8YBurQw47FEbARpp2L-_6NZsnlyVb3K4NxIn7cv0EpNQn78Mr1m5s0PzagzpF6CINq4jANJ1RQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
