I suspect that recon-all is confused about your SUBJECTS_DIR: setenv SUBJECTS_DIR /home/[email protected]/freesurfer_output<mailto:/home/[email protected]/freesurfer_output>
Can you change SUBJECTS_DIR to not include the special characters ‘@’ and ‘.’? From: andrew cardona <[email protected]> Sent: Thursday, June 26, 2025 1:13 PM To: Freesurfer support list <[email protected]> Subject: [Freesurfer] Re: Trouble shooting External Email - Use Caution Hi, thank you for your timely response! this is the output for recon all :s-check-version --s sub-SM --o /tmp/tmp.db9lL9 Thu Jun 26 10:38:52 EDT 2025 setenv SUBJECTS_DIR /home/[email protected]/freesurfer_output<http://secure-web.cisco.com/1XhN7J0uWpbJu5P6U-KWW7_vFKqPR1_b5_p2oNxiWiLLAIHIb3TdFljEiR1kxmCkoFkzpDw7TyUVXpp6R7gGXJuu-bJsQj2EY2sF6qpweLd5XayPOTCiHPQ2OIQXtBlKdfLUqmJu-WvqMVoA2beFbvuBrHdTBj43evmn8EqzjFZlimt9LRM0uZnjC1p9F6bn_dktaXREcBZfvvV6_CRBBu2VsMALJ3q6hdPPqHQq52G3PoEVOuUZEjb9b6Q4XiwQzZD3qje2zafZiuLkeo097fP47WLtnEOzsM1Hg7dGKBlzaGwtIxsPafZk1hCHLtXM9UAY1qYIk86hxEEozJeR3zA/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output> cd /home/[email protected]<mailto:[email protected]> /home/[email protected]/freesurfer/bin/fs-check-version<http://secure-web.cisco.com/1pJl-Z0s2V0EQBXcI7RPHclu351mpd6hX1EwAv_D0Y3IqF4it_unBLSRy9xzUKUgRFytaYSyk_fVmLVfOjLL_rQ1cQ9Si8K8gjZLmQbNWhTUvxebktRz6xjneHW5OTw3jtR6n20nr6QR9SWM_QjwfaA3tmgidXP0JCnOMMhr1Oq8_2ghCt7b-fGtqceeG_WXU9Ai0nveaEf6bENsTpdWjvSxMcyArjVkl_VRGhwlHej_DH78OAhBqYGyuGUh94V97lIjNox05nVrRmHNvgvUD6XN7Ny_geDO1_wfC_OPH02ObRfC1ReNWWom8fSHBRTVGXEu1h_jnazISy9joOKe_fA/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer%2Fbin%2Ffs-check-version> --s sub-SM --o /tmp/tmp.db9lL9 -rwxr-xr-x 1 tur31606 domain users 18565 Jun 13 2023 /home/[email protected]/freesurfer/bin/fs-check-version<http://secure-web.cisco.com/1pJl-Z0s2V0EQBXcI7RPHclu351mpd6hX1EwAv_D0Y3IqF4it_unBLSRy9xzUKUgRFytaYSyk_fVmLVfOjLL_rQ1cQ9Si8K8gjZLmQbNWhTUvxebktRz6xjneHW5OTw3jtR6n20nr6QR9SWM_QjwfaA3tmgidXP0JCnOMMhr1Oq8_2ghCt7b-fGtqceeG_WXU9Ai0nveaEf6bENsTpdWjvSxMcyArjVkl_VRGhwlHej_DH78OAhBqYGyuGUh94V97lIjNox05nVrRmHNvgvUD6XN7Ny_geDO1_wfC_OPH02ObRfC1ReNWWom8fSHBRTVGXEu1h_jnazISy9joOKe_fA/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer%2Fbin%2Ffs-check-version> freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 $Id$ Linux CLA19571.tu.temple.edu<http://secure-web.cisco.com/1t_7Rm4lTvqpfznABOb5h1rMYLZffPskvanwkVtCj5cxLcnSt_bfy8OBRRk9hvWlF58CicP1LZ-ghsZlQ24OKaXzXfXK8POYc_rNOk6jAW9g1wONvNmYJWC5K5K5jyVDvP1NfGmtZwazzMbqh77Yl_Jguytj0vSpVg-mJw9j3DFzq9NDM5VVs6tIyN08KzE3TxnX9Vt9tj6SfPud7_JFVKkys8U6HQSav-nKbzZ3BSY1m-77tHPcsJUT39y1B_47y6vJvyr5XCCc1Iefyp_zfcwEJiama_aDXnhJjG9CqgeFy5N5ZrdBIN85vsyD-EoGw5-D7AeaqnE5NAcpJl1P9kg/http%3A%2F%2FCLA19571.tu.temple.edu> 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux pid 79136 Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /home/[email protected]/freesurfer/build-stamp.txt<http://secure-web.cisco.com/1m4ueHIuKAwHh5_5L2UNIW3Os0ozpoalU_a5ZSYjD_3X-YmYDZ5C1WAwO8VtCQUTDtTpgjkReZQS4q3fgmSPuS24q7dHz2stUj4Ee_AC0sSylLYQeJ46P7-FE-3e7tP8p0USBXrGxJlTnTq8hQKvAlAV8MEi3sGsuzy_tgySodL13-JkNHORC3cMZaXpOF4tBcXTQWAetrVS7C2qPerYCSJ1ZuKGE3_pjKkbA6XAxl-Zz7XeHJSsXiqXlFRVW-p8jZW9PY1vRubmj4ZwZK_Dme9RNsaHjNluUHV_cz41UorrkL8LJlT4LOMSH4dJpILmmCqavb7HSolO7hWBeEtm3Rw/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer%2Fbuild-stamp.txt> Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/[email protected]/freesurfer_output<http://secure-web.cisco.com/1XhN7J0uWpbJu5P6U-KWW7_vFKqPR1_b5_p2oNxiWiLLAIHIb3TdFljEiR1kxmCkoFkzpDw7TyUVXpp6R7gGXJuu-bJsQj2EY2sF6qpweLd5XayPOTCiHPQ2OIQXtBlKdfLUqmJu-WvqMVoA2beFbvuBrHdTBj43evmn8EqzjFZlimt9LRM0uZnjC1p9F6bn_dktaXREcBZfvvV6_CRBBu2VsMALJ3q6hdPPqHQq52G3PoEVOuUZEjb9b6Q4XiwQzZD3qje2zafZiuLkeo097fP47WLtnEOzsM1Hg7dGKBlzaGwtIxsPafZk1hCHLtXM9UAY1qYIk86hxEEozJeR3zA/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output> Actual FREESURFER_HOME /home/[email protected]/freesurfer<http://secure-web.cisco.com/1bcBvAu03Y6cV5vW2FOrE3Nv2-jyb-sy9I4SwmPBI4NjYLRCb_ldP8wOv9VZueml4xTP9NUS1NWhi1B_jur2V3796BwPyb-3YremcA2lsiMMY_4-qrZEOu4TPNqVkFjqhgEvnSPVcRhPwY3-FWnWiUIWXwPhG54lXlytPT1FR-0jqekBhquGqJuPWO30E6y3GVIf7Wgbod27bsCz-QkLGhwopQFScCN2959FZNA6zgcauWD7eE0fLQ-Bn43lI9X4uYkei3VqlU2d-PRa_9v9Iam7gU_p6eJ6-zUltR2t_JHrcb8QrKDLg0ZrO25XQcHeFc_kuFIHTZkcz325qu-0GXw/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer> Linux CLA19571.tu.temple.edu<http://secure-web.cisco.com/1t_7Rm4lTvqpfznABOb5h1rMYLZffPskvanwkVtCj5cxLcnSt_bfy8OBRRk9hvWlF58CicP1LZ-ghsZlQ24OKaXzXfXK8POYc_rNOk6jAW9g1wONvNmYJWC5K5K5jyVDvP1NfGmtZwazzMbqh77Yl_Jguytj0vSpVg-mJw9j3DFzq9NDM5VVs6tIyN08KzE3TxnX9Vt9tj6SfPud7_JFVKkys8U6HQSav-nKbzZ3BSY1m-77tHPcsJUT39y1B_47y6vJvyr5XCCc1Iefyp_zfcwEJiama_aDXnhJjG9CqgeFy5N5ZrdBIN85vsyD-EoGw5-D7AeaqnE5NAcpJl1P9kg/http%3A%2F%2FCLA19571.tu.temple.edu> 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux /home/[email protected]/freesurfer_output/sub-SM<http://secure-web.cisco.com/1bxbKXeYgEtQILqM1_ybI3OzzZew47atkj1yCnjWp-TK6h7qQH67_YHemSoKYMoVe-wqfzuOBRA6H5UXcnYEqUletjs3ctbmdQBEQab1_hfDslU-2obSF3mc9goKWSXx5NfH39tp6a1asTMgEiqc1oQgUC8ZFp9HSE1k41Si8HRUseSJ153jFp2Vqwg0vWM2mPp4dKv6RR2nxry5x-SCARFsi1usUfNrEtzlU8svIEDyQAjyHLNdgQE0yS_QbnkIIuJUwzsVgt9-p2vnJFxPmfoCz1s-AY1JAxaylk984Fx3GdQXImF1Tmja3Qwpddm4-VNF9ewMdcIdMcs4V4e5CIw/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-SM> mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-SM/sub-10317_T1w.nii.gz /home/[email protected]/freesurfer_output/sub-SM/mri/orig/001.mgz<http://secure-web.cisco.com/1EbRQq-UzC6X6385LteWkBEQh3Ucg6zQVQITO7ib9KS8uJMBsTWgnheFA57F7hCPRsDiQ38nPttFzp64hh8YioD9EjWaSg7yLuawMMvbQywdAUHw8q38iZ_0RIacqIB_F4x6DZkjBsfOsqSqUlOQ3L-7lvWVo-LfT-mJoJ_h7b-9DsIaN-vhwyQvfJlzM28yBLzR1yh4KCOanAwkhI18R6GhGqOrDONS0LXefoyx4rSjeCdim0DOT-xf3FuUbsDX9N-8nq6zi-HPZARjzQBhhchZgmy6duX3rpHrOfZ5bSdqJs0cVoS-45fmQOjVGt5qVD3wzwc_IxsZr9PYWrK1Jig/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-SM%2Fmri%2Forig%2F001.mgz> mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-SM/sub-10317_T1w.nii.gz /home/[email protected]/freesurfer_output/sub-SM/mri/orig/001.mgz<http://secure-web.cisco.com/1EbRQq-UzC6X6385LteWkBEQh3Ucg6zQVQITO7ib9KS8uJMBsTWgnheFA57F7hCPRsDiQ38nPttFzp64hh8YioD9EjWaSg7yLuawMMvbQywdAUHw8q38iZ_0RIacqIB_F4x6DZkjBsfOsqSqUlOQ3L-7lvWVo-LfT-mJoJ_h7b-9DsIaN-vhwyQvfJlzM28yBLzR1yh4KCOanAwkhI18R6GhGqOrDONS0LXefoyx4rSjeCdim0DOT-xf3FuUbsDX9N-8nq6zi-HPZARjzQBhhchZgmy6duX3rpHrOfZ5bSdqJs0cVoS-45fmQOjVGt5qVD3wzwc_IxsZr9PYWrK1Jig/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-SM%2Fmri%2Forig%2F001.mgz> mri_convert: can't determine type of output volume Command exited with non-zero status 1 @#@FSTIME 2025:06:26:10:38:53 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 50% M 6144 F 0 R 270 W 0 c 0 w 2 I 0 O 0 L 0.18 0.27 0.34 @#@FSLOADPOST 2025:06:26:10:38:53 mri_convert N 2 0.18 0.27 0.34 Linux CLA19571.tu.temple.edu<http://secure-web.cisco.com/1t_7Rm4lTvqpfznABOb5h1rMYLZffPskvanwkVtCj5cxLcnSt_bfy8OBRRk9hvWlF58CicP1LZ-ghsZlQ24OKaXzXfXK8POYc_rNOk6jAW9g1wONvNmYJWC5K5K5jyVDvP1NfGmtZwazzMbqh77Yl_Jguytj0vSpVg-mJw9j3DFzq9NDM5VVs6tIyN08KzE3TxnX9Vt9tj6SfPud7_JFVKkys8U6HQSav-nKbzZ3BSY1m-77tHPcsJUT39y1B_47y6vJvyr5XCCc1Iefyp_zfcwEJiama_aDXnhJjG9CqgeFy5N5ZrdBIN85vsyD-EoGw5-D7AeaqnE5NAcpJl1P9kg/http%3A%2F%2FCLA19571.tu.temple.edu> 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-SM exited with ERRORS at Thu Jun 26 10:38:53 EDT 2025 For more details, see the log file /home/[email protected]/freesurfer_output/sub-SM/scripts/recon-all.log<http://secure-web.cisco.com/1p2VY7d_X78eme-xCA5Sd1V2yrW6Twm-0Ku6RuNHXWikCX4L0jrBi-6C8_oOGsve5UxtTU5t8uQnZJ8pqGa67hn1X6DlHJ58xsySXLSiYMKMMDoSgmzid_CgU-o1u8j8pFEKsvAU39D8bn3vjvF-6xOXAEM2o-7FeoPuBFrB0wWieTxXe6NOfpxI5fMTJmR-1lwShVq2Lau4pCmoDQ8tdxH1c97-GPZm44gdW4xq0KQbT3QjXjSq4OJTSNwXJKxQdnoEefqqHHfzYCxnsF7f6ojGJbUAdQR870dnAKPweHzpm3cFJuWPXaMW69dpMg92_M-ba2O_dHYT8EtWmzGdq5g/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-SM%2Fscripts%2Frecon-all.log> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/1bIy1V8oCXJ6N7-8j_BAuYjF1WVMCPXaZ-KbHzsWFL8t0Fdrk1u4KEFucBf3Uy2f_PxaYV8BIOX1QmncFUj9yy03pguvx-iu1N1JBuZfKM3_dicdBnUtdstMhj5v0Yzohr7kKZFDC9noBUk1C_gOCFp-V0LzTUKt14UhNHpPlZ2YjwNe4QdG4wiU-yVgTQLYomZ0qA0qyFnwAM51Qf1ErJ8cHdaL68J4tvWO8AO5PA856RZ155jWDWFZaXn-yCWkiVtsb9pdZLXCLhqNACHhy2eWs4bUpraT2tVFDIN-h2h3mzG0sIWCdd9qQAfjbyA0TSKQ2Nw0ni5jE1DYOS6UGww/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting> and for mri_info it just reports back all the stats of the file it has no issue reading it when using mri_info. best, andrew On Thu, Jun 26, 2025 at 12:14 PM Huang, Yujing <[email protected]<mailto:[email protected]>> wrote: If you run mri_info on the image, what does it report? Can you send recon-all.log? Yujing From: andrew cardona <[email protected]<mailto:[email protected]>> Sent: Thursday, June 26, 2025 11:17 AM To: [email protected]<mailto:[email protected]> Subject: [Freesurfer] Trouble shooting External Email - Use Caution Good morning, I am trying to troubleshoot one participant, yet It keeps failing and starting this error “ mri_convert : can’t determine type of output volume” we have tried changing the file manually to mgz and it works yet when running recon all it crashes. Any guidance would be appreciated! Thank you in advance! Best, Andrew cardona _______________________________________________ Freesurfer mailing list -- [email protected]<mailto:[email protected]> To unsubscribe send an email to [email protected]<mailto:[email protected]> https://mail.nmr.mgh.harvard.edu/mailman3/lists/[email protected]/<https://secure-web.cisco.com/1Ouvu_IQunqAroRmyoVCmiOYUTFLYmJYjRLZfXn76muVf-csp0p8N3IB8jRJR-f268CHp3q3TDR2PdIX7-POfDgatQOnzUdnSde-46Qq0u2LeVl_-FpaMwp51y0JyFK-lpVUh25RCFnkuPZsp7LcwzMS6EC5Xfxl55PJVvWgLnl0jwMxjLI_hZqHl2lcycmhoyGEVAyfAqP7FCwpmthiVdmgErNXx_Xo4L2F56UGcW2IS0GiLtMewHI4nth4ReE99ECtNJ0osLR2wlqTFfyywjKGu9RYl06rWwykeUQps8y339njdq8xcmhuINMqAD3U1kjD-dHPteKra5VLfyD0Rmw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> 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://secure-web.cisco.com/1TAhWc2XH1laNXfxT0QT6kan_Ds79Umko0SppIqMGQyWAAssX88a6fP1iQdJXvrWLmQ0BWRd2bGQEBRE220544cYaJPMNlQSQZCed4aiO_iXRuwtSKAtndW46kZKywerRYOI0AYtFQdKsmsrxytlVj9kgenJ8XJBrRAIUcbGVczUlHliiSAQMyf_jpf_4sGc2gl89T9_-D4z9dzkxJrL_Tty8ByX3O0dRS-W3W3mEZB0mS3z-dzd9p68PwdVggTTHNfxqnLLoW4L2ivx1cJCI9iEJbouxnHtYasJHGpxkp4RPUf0DK3-fhLhmKwEyYG5q59c__Ev-mjJb8EUQCKF0MQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1TAhWc2XH1laNXfxT0QT6kan_Ds79Umko0SppIqMGQyWAAssX88a6fP1iQdJXvrWLmQ0BWRd2bGQEBRE220544cYaJPMNlQSQZCed4aiO_iXRuwtSKAtndW46kZKywerRYOI0AYtFQdKsmsrxytlVj9kgenJ8XJBrRAIUcbGVczUlHliiSAQMyf_jpf_4sGc2gl89T9_-D4z9dzkxJrL_Tty8ByX3O0dRS-W3W3mEZB0mS3z-dzd9p68PwdVggTTHNfxqnLLoW4L2ivx1cJCI9iEJbouxnHtYasJHGpxkp4RPUf0DK3-fhLhmKwEyYG5q59c__Ev-mjJb8EUQCKF0MQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
_______________________________________________ Freesurfer mailing list -- [email protected] To unsubscribe send an email to [email protected] https://mail.nmr.mgh.harvard.edu/mailman3/lists/[email protected]/ 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.
