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