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Thank you very much.

On Tue 24 Mar, 2020, 11:14 PM Hoopes, Andrew, AHOOPES@mgh.harvard.edu wrote:

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

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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer