I suspect that recon-all is confused about your SUBJECTS_DIR:
setenv SUBJECTS_DIR
/home/tur31...@tu.temple.edu/freesurfer_output<mailto:/home/tur31...@tu.temple.edu/freesurfer_output>
Can you change SUBJECTS_DIR to not include the special characters ‘@’ and ‘.’?
From: andrew cardona <ascardona0...@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/tur31...@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/tur31...@tu.temple.edu<mailto:tur31...@tu.temple.edu>
/home/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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://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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@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 <ascardona0...@gmail.com<mailto:ascardona0...@gmail.com>>
Sent: Thursday, June 26, 2025 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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