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 rdacostaa@gmail.com wrote:
External Email - Use CautionHi 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 nayanw775@gmail.com wrote:
External Email - Use CautionDear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${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 paul@corticometrics.com wrote:
External Email - Use CautionSure 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 < rdacostaa@gmail.com> wrote:
External Email - Use CautionHi 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 paul@corticometrics.com wrote:
External Email - Use CautionHi 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 < rdacostaa@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/1QkqmryHlmSo2BLsXA4nDfN2RPHoO3L1I9knuOQHCp57aga... > 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 < > rdacostaa@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_t... >> 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... > 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH... 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_72InTeP44q6rQ36vfXOBkAylKoBmfD4UYDpwNH...