I'm wondering how you ran recon-all. Do you see the error even running it w/o any arguments?
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> Sent: Friday, January 19, 2024 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Peled, Noam,PhD Sent: Friday, January 19, 2024 2:42 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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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