External Email - Use Caution I don’t see what FREESURFER _HOME is set to, but if you used the .deb package installer, it would be /usr/local/freesurfer/7.4.0, i.e. $ wget https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all queries ….,.. output deleted ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted … $ which recon-all /usr/local/freesurfer/7.4.0/bin/recon-all $ recon-all -version freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e If you used the tar file instead, then some permissions might not be correct depending upon how/where it was unarchived (and some dependencies might be missing). - R.
On Jan 19, 2024, at 15:20, Peled, Noam,PhD <[email protected]> wrote:I'm just trying now to run the "recon-all -version", also without any arguments. Both produce the same error.Thanks!NoamFrom: [email protected] <[email protected]> on behalf of Huang, Yujing <[email protected]>Sent: Friday, January 19, 2024 3:10 PMTo: Freesurfer support list <[email protected]>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: [email protected] <[email protected]> On Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:59 PMTo: Freesurfer support list <[email protected]>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,NoamFrom: [email protected] <[email protected]> on behalf of Huang, Yujing <[email protected]>Sent: Friday, January 19, 2024 2:54 PMTo: Freesurfer support list <[email protected]>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: [email protected] <[email protected]> On Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:42 PMTo: [email protected]: [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 _______________________________________________Freesurfer mailing [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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