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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:

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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:

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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:

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Following this more actualized link: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

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://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation

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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