Hi Koustav,

 

My guess is you have not correctly ‘sourced’ freesurfer (made it available in your shell environment). Following the ‘Setup & Configuration’ steps in the FS download page, you should always run the following before using freesurfer:

 

export FREESURFER_HOME=/usr/local/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh

 

Hope that helps,

Andrew

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koustav Chatterjee <chatterjeekoustav@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Saturday, March 21, 2020 at 9:35 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all : command not found

 

        External Email - Use Caution        

Dear Sir/Madam,

 

Hope this mail finds you well, considering the present pandemic scenario across globe.

 

I have installed FreeSurfer in my PC successfully and I have been following tutorials and freesurfer wiki to learn the basics of it.

I have an image with .nii extension saved in usr/local/freesurfer/subjects directory in ubuntu.

I wanted to use recon-all command for preprocessing the image.nii.

 

root@ubuntu:/usr/local/freesurfer/subjects# recon-all -s kctest01 -i (the input file.nii) 

the result shows, recon-all: command not found

 

It would be kind enough if you could please help me out.

 I am also sharing the screen shot of the terminal window I used for this programming, if it would e of any help.

 

Thank you,

Best regards,

Koustav

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