External Email - Use Caution
Thanks!!!
Kind regards, Rosie
El mié., 7 jul. 2021 21:32, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionHi Rosie,
In that case, you can try running the v6 version of hippocampal subfields, e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I made some corrections (control points,...). I just want the hipocampal subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul Wighton paul@corticometrics.com escribió:
External Email - Use CautionThanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is not in this version.
There are two options. If you want to continue using v6.0.0, you can refer to the instructions here: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1rLyfwTNMrD8uPGQPvaKYcfc7uDe6gWOoA1V_iVTwU9RHJm... https://secure-web.cisco.com/1yG2oNYO-Rk8MmvOxXyxAXK4xUf0I1w4DLd-6h6jEgglbgaEu_bTXvX6ZZCH-CJjPD9OFaIQLCe3ifyaJhyDl1D0zzu2FxEKkYiL7ORLQBuGkPlxhMHNO_fjTLguHjY0470nArGjzSNK_okSRQR36E06HStZjHAzrPyNFRofrqANGoW0OlMSFsJRiFZkqOOetHjGUx45LipBooxBUq1N2m679dT0cWGbgNBd3ZGMfbd90aICTFZQ8KoXaWy7vcgXaDW6e3vulDZ9jrSwFH8ifZQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields
Otherwise, if you upgrade to the latest version (v7.1.1) you can use the segmentHA_T1.sh script.
-Paul
On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo < rdacostaa@gmail.com> wrote:
External Email - Use CautionHere it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file or directory rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton paul@corticometrics.com wrote:
External Email - Use CautionOk, 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 Caution > > Dear Rosalia, > > Once you export and source freesurfer with the following commands > > export FREESURFER_HOME=/usr/local/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > type sh > after sourcing and then try running it(without closing the > terminal) hopefully, it will work that way. > > Thanks and Regards > Nayan Wadhwani > > > On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < > rdacostaa@gmail.com> wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> I did it: >> >> # FREESURFER >> export FREESURFER_HOME=/usr/local/freesurfer >> export PATH=${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 < >> paul@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 < >>> rdacostaa@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 < >>>> paul@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 < >>>>> 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/1UOXPN9Y_Lpnff1I-uWNXLM-VvbTewnSXhiAnzvlaEJ3DKS... >>>>>> 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/1O-IsozxKzMa7OW1F4vkS4Gq--QMEHhSpc2SRUgUumNKUxZ... >>>>>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >>> 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/1WRzSMrHqmt69kko1IETjHEuf7S-USSnowIkVOH35q5jf2F... >> 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