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 cd /home/tur31...@tu.temple.edu /home/ tur31...@tu.temple.edu/freesurfer/bin/fs-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 freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 $Id$ Linux CLA19571.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 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 Actual FREESURFER_HOME /home/ tur31...@tu.temple.edu/freesurfer Linux CLA19571.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 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 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 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 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 To report a problem, see 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/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://secure-web.cisco.com/1TAhWc2XH1laNXfxT0QT6kan_Ds79Umko0SppIqMGQyWAAssX88a6fP1iQdJXvrWLmQ0BWRd2bGQEBRE220544cYaJPMNlQSQZCed4aiO_iXRuwtSKAtndW46kZKywerRYOI0AYtFQdKsmsrxytlVj9kgenJ8XJBrRAIUcbGVczUlHliiSAQMyf_jpf_4sGc2gl89T9_-D4z9dzkxJrL_Tty8ByX3O0dRS-W3W3mEZB0mS3z-dzd9p68PwdVggTTHNfxqnLLoW4L2ivx1cJCI9iEJbouxnHtYasJHGpxkp4RPUf0DK3-fhLhmKwEyYG5q59c__Ev-mjJb8EUQCKF0MQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1TAhWc2XH1laNXfxT0QT6kan_Ds79Umko0SppIqMGQyWAAssX88a6fP1iQdJXvrWLmQ0BWRd2bGQEBRE220544cYaJPMNlQSQZCed4aiO_iXRuwtSKAtndW46kZKywerRYOI0AYtFQdKsmsrxytlVj9kgenJ8XJBrRAIUcbGVczUlHliiSAQMyf_jpf_4sGc2gl89T9_-D4z9dzkxJrL_Tty8ByX3O0dRS-W3W3mEZB0mS3z-dzd9p68PwdVggTTHNfxqnLLoW4L2ivx1cJCI9iEJbouxnHtYasJHGpxkp4RPUf0DK3-fhLhmKwEyYG5q59c__Ev-mjJb8EUQCKF0MQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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