On Wed, Jul 7, 2021 at 8:17 PM Paul Wighton <paul@corticometrics.com> wrote:

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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:
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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 <nayanw775@gmail.com> wrote:
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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:
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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:
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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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