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Dear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh after sourcing and then try running it(without closing the terminal) hopefully, it will work that way.
Thanks and Regards Nayan Wadhwani
On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo rdacostaa@gmail.com wrote:
External Email - Use CautionHi Paul,
I did it:
# FREESURFER export FREESURFER_HOME=/usr/local/freesurfer export PATH=${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 CautionFollowing this more actualized link: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1GkrlAYjqlnbk3q7VX5LLmcVI9cUDcfMnFG1fucd4TA6hgS... 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/10sqb1n1jGOzAGOp6CyM7XBr18SydqsBY5vjjg7mlweYDJ8... 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
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