External Email - Use Caution
possibly the only thing is I am remote accessing through my university so my terminal automatically opens with the @
On Thu, Jun 26, 2025 at 1:19 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
I suspect that recon-all is confused about your SUBJECTS_DIR:
setenv SUBJECTS_DIR /home/tur31606@tu.temple.edu/freesurfer_output
Can you change SUBJECTS_DIR to not include the special characters ‘@’ and ‘.’?
*From:* andrew cardona ascardona0908@gmail.com *Sent:* Thursday, June 26, 2025 1:13 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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/tur31606@tu.temple.edu/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/tur31606@tu.temple.edu /home/ tur31606@tu.temple.edu/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/tur31606@tu.temple.edu/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/ tur31606@tu.temple.edu/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/tur31606@tu.temple.edu/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/tur31606@tu.temple.edu/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/ tur31606@tu.temple.edu/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/ tur31606@tu.temple.edu/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/ tur31606@tu.temple.edu/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/ tur31606@tu.temple.edu/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://secure-web.cisco.com/1cRTWDBiR_wUBTTgQqUoyT7Y7Mj4mZLlio-JZKDX4STd30fG... 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 YHUANG43@mgh.harvard.edu wrote:
If you run mri_info on the image, what does it report?
Can you send recon-all.log?
Yujing
*From:* andrew cardona ascardona0908@gmail.com *Sent:* Thursday, June 26, 2025 11:17 AM *To:* freesurfer@nmr.mgh.harvard.edu *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
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