External Email - Use Caution Yes, it's all sourced correctly. The output after sourcing:
bash:/opt/freesurfer/freesurfer-7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer/freesurfer-7.4.1 FSFAST_HOME /opt/freesurfer/freesurfer-7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/freesurfer-7.4.1/subjects MNI_DIR /opt/freesurfer/freesurfer-7.4.1/mni Is your Freesurfer Environment sourced correctly? Here is the wiki help https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Gregory Book Sent: Tuesday, April 23, 2024 9:21 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Problem running recon-all External Email - Use Caution I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error: -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file not found Paths are all set, and all scripts and executables have execute permissions. What might be happening? _______________________________________________ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1csRj5QjHjBcNMSF5ZdSm_KFjj2CdCWqkNIeDVnTqmNRvCVjO_-uW6ilDiK7dYqY3PVaVlIlywlOo2D-3glzp3Th0lB8BNXisYolGza5Eq5X5wFRhI8WvDqG6UlWp9ZJCStN6wi1cCZyeJliYQ4BOWuVGVyIVC7FqIwbY9iGwtWa9vsO45tQ2X9M11LKqMTVreklJFna4BIejHR75p1nFAiZL-6gp1f4eiHaTMepxp6ja_fVwLcDP6PBy-tce1TqvJFGlWqSI7UpYxa6i8m4yyPwFqMaGzXpAGJmGlr13mce88KtZVxpFe3pf7JrfUgNkEx0kANR7wmUCJt3884-GNA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/1csRj5QjHjBcNMSF5ZdSm_KFjj2CdCWqkNIeDVnTqmNRvCVjO_-uW6ilDiK7dYqY3PVaVlIlywlOo2D-3glzp3Th0lB8BNXisYolGza5Eq5X5wFRhI8WvDqG6UlWp9ZJCStN6wi1cCZyeJliYQ4BOWuVGVyIVC7FqIwbY9iGwtWa9vsO45tQ2X9M11LKqMTVreklJFna4BIejHR75p1nFAiZL-6gp1f4eiHaTMepxp6ja_fVwLcDP6PBy-tce1TqvJFGlWqSI7UpYxa6i8m4yyPwFqMaGzXpAGJmGlr13mce88KtZVxpFe3pf7JrfUgNkEx0kANR7wmUCJt3884-GNA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
