On Jan 19, 2024, at 15:20, Peled, Noam,PhD <NPELED@mgh.harvard.edu> wrote:

I'm just trying now to run the "recon-all -version", also without any arguments. 

Both produce the same error.

Thanks!

Noam

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Friday, January 19, 2024 3:10 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

 

I’m wondering how you ran recon-all.  Do you see the error even running it w/o any arguments?

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

 

Thanks Yujing,

Yes, I looked for the file permissions using ls -l. It does have execute permissions.

I also tried running chmod which didn't help.

 

Thanks,

Noam

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

 

After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.

 

1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission

 

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found

 

Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 (freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found

 

Other functions, e.g. freeview, mri_info, all seem to work as expected

 

Would love some help.

Thanks,

Noam

 

 

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