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 <yhuan...@mgh.harvard.edu> wrote: > I suspect that recon-all is confused about your SUBJECTS_DIR: > > setenv SUBJECTS_DIR /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 /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://secure-web.cisco.com/1cRTWDBiR_wUBTTgQqUoyT7Y7Mj4mZLlio-JZKDX4STd30fGPAOEWpo0wD2Nt_AMuR-eFqYuc9HnA9MsbkFK2rhQgBmD2eqSs6WQ_7KTn0V4WLFZ4-B8HLSgwZLkQBcjpenbgqKmOXGwkC7_HQpq1DinqoS6AeCrgX18h3Dxbgy1-aargGF3cOp0lS-iKbkOxDHBEbVlbqm2siB1tCnyFn3S-Wg7EbdUT4QY86Lag20cDxsHsvRXVdP8VrLoY6W-JeQua2_pQQ4_41Pkeamk2h2b4rrUC52Zu1IIcKChDzh8oPQ0DeUk6Rybe0lLEBVa4odGWpSl3wDTZ5xVQHuA7Dg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting > <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> > 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> > *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 > > _______________________________________________ > Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu > To unsubscribe send an email to freesurfer-le...@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/1qEA32uYotMIOwzL8BXfGTccwSgpGVBJWFx0QXT-fUk_4Tb9kFkgd2UZxGhEAL7wFr6-gMa-6vHCqAdFTW1qg75yVNrmvxm5Rn4vrmSyefQBtoW1eLVER8Yl2SEA_MDmuv-oSNEbdLqOlb7tStZJbd-E_tcfVMlKQmX0BBsID2KlnHza_GdH7vAu8n0jqL2o5vU1aAg4sGbIMQnL6g4vhC4kvv2jPbqjCPHvmSBO7VvZj97K4SeLe02-FCMGbkbj-EY7242N-r79GlAk7mlV2F2rtq3B-isBm1542rCMdZRhzD29m17YXOh0NN_DEB6TgLuXkcs7kw3TkgkpLWIRMTQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F > <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. 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