External Email - Use Caution
Good afternoon, I am reaching out as I am trying to trouble shoot one participant, yet it keeps failing and stating the same error "mri_convert: cant determine type of output volume" we have tried changing the file manually to mgz and it works yet when we run recon all it crashes. We also can run mri_info on the file perfectly fine, we also uninstalled and reinstalled freesurfer itself. Any guidance would be greatly appreciated, thank you!
*This is what is outputted when running recon all: * Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ Wed Jul 2 11:36:48 EDT 2025
setenv SUBJECTS_DIR /home/tur31606@tu.temple.edu/freesurfer_output cd /home/tur31606@tu.temple.edu /usr/local/freesurfer/8.0.0/bin/fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ -rwxr-xr-x 1 root root 18565 Feb 3 20:30 /usr/local/freesurfer/8.0.0/bin/fs-check-version
freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a $Id$ 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 451741 Current FS Version freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a Subject does not have a bstampfile, copying /usr/local/freesurfer/8.0.0/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a 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 Actual FREESURFER_HOME /usr/local/freesurfer/8.0.0 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/tur31606@tu.temple.edu/freesurfer_output/sub-1009
mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz
mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz mri_convert: can't determine type of output volume Command exited with non-zero status 1 @#@FSTIME 2025:07:02:11:36:49 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 100% M 6144 F 0 R 270 W 0 c 0 w 2 I 0 O 0 L 0.30 0.56 0.42 @#@FSLOADPOST 2025:07:02:11:36:49 mri_convert N 2 0.30 0.56 0.42 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-1009 exited with ERRORS at Wed Jul 2 11:36:49 EDT 2025
For more details, see the log file /home/ tur31606@tu.temple.edu/freesurfer_output/sub-1009/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1lZL5fd1-LIJV20MkpYIehpHZ9KjK6NT_O2y2M8boj9gcNFl...
Best, Andrew Cardona
I think the problem may be the @ in the path. It is uncommon to have @s in the linux path. Can you remove it?
On 7/2/2025 11:45 AM, andrew cardona wrote:
External Email - Use Caution
Good afternoon, I am reaching out as I am trying to trouble shoot one participant, yet it keeps failing and stating the same error "mri_convert: cant determine type of output volume" we have tried changing the file manually to mgz and it works yet when we run recon all it crashes. We also can run mri_info on the file perfectly fine, we also uninstalled and reinstalled freesurfer itself. Any guidance would be greatly appreciated, thank you!
*This is what is outputted when running recon all: * Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ Wed Jul 2 11:36:48 EDT 2025
setenv SUBJECTS_DIR /home/tur31606@tu.temple.edu/freesurfer_output http://secure-web.cisco.com/1hS-6aZ9YCr9n7TGX59rQpf9K2nwjFnq1Dv0MfUWFfwrIRtvDOeoJEzTLSTINZLpIAy45wJ2rcMfToXhVmoI_s2JyjzfZ8OwzkJaGdrQRtkjQkoQQ8E4bwHSZ5-LwHdPhfR88y9kye5fqJW2sDMFM-J9DzGao99anll-9DGrtlgXImQ1wZVVE0jS9zdKEw6_yyBmhmypzCqjmDEAw8mwZAGZmlAwclScjXtZjkprkLfl8l4dXxF0yExrbcRwsMxN2QOnul0ikrSlSKswymVgH71KgC1ErJYmocGKAiTlrn3p0uAWSghBZfp-hzZAPGeC8XbDmngbckkCmEe6pitIcWw/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output cd /home/tur31606@tu.temple.edu /usr/local/freesurfer/8.0.0/bin/fs-check-version --s sub-1009 --o /tmp/tmp.oai3VJ -rwxr-xr-x 1 root root 18565 Feb 3 20:30 /usr/local/freesurfer/8.0.0/bin/fs-check-version
freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a $Id$ Linux CLA19571.tu.temple.edu http://secure-web.cisco.com/1KjMhilgbPgI1ewd6dc-xXVQOGsJEbrGHz_GGegclf7cbDZYz4by_iJTwIbIKlJRghYUhGynnaVNe7wYyIH0ojoyouXcp3UKYqnQJgn7LlLmP-MRa6akR4Y4nWwzCL0NR_A4__GHOWnHTG51ogXI7-memKhTQliPXFj0Crz-e1bpIuvu3J497rRwl9HK20x6BqSP5dw6ifwX_vvODFKRLJXEtoUUfVa7nhq3kSMG3YsP_vL3m-BPu5ePPMH8WIHulr3XgKPe-tBzsd_HOA1J1d8cIr4V9V6XPZ4oMWzgnD-aduAtw8vGZwhsDuKal3jOpkgPR0cTKPKz11ZDm7j9qXQ/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 451741 Current FS Version freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a Subject does not have a bstampfile, copying /usr/local/freesurfer/8.0.0/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a 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/1hS-6aZ9YCr9n7TGX59rQpf9K2nwjFnq1Dv0MfUWFfwrIRtvDOeoJEzTLSTINZLpIAy45wJ2rcMfToXhVmoI_s2JyjzfZ8OwzkJaGdrQRtkjQkoQQ8E4bwHSZ5-LwHdPhfR88y9kye5fqJW2sDMFM-J9DzGao99anll-9DGrtlgXImQ1wZVVE0jS9zdKEw6_yyBmhmypzCqjmDEAw8mwZAGZmlAwclScjXtZjkprkLfl8l4dXxF0yExrbcRwsMxN2QOnul0ikrSlSKswymVgH71KgC1ErJYmocGKAiTlrn3p0uAWSghBZfp-hzZAPGeC8XbDmngbckkCmEe6pitIcWw/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output Actual FREESURFER_HOME /usr/local/freesurfer/8.0.0 Linux CLA19571.tu.temple.edu http://secure-web.cisco.com/1KjMhilgbPgI1ewd6dc-xXVQOGsJEbrGHz_GGegclf7cbDZYz4by_iJTwIbIKlJRghYUhGynnaVNe7wYyIH0ojoyouXcp3UKYqnQJgn7LlLmP-MRa6akR4Y4nWwzCL0NR_A4__GHOWnHTG51ogXI7-memKhTQliPXFj0Crz-e1bpIuvu3J497rRwl9HK20x6BqSP5dw6ifwX_vvODFKRLJXEtoUUfVa7nhq3kSMG3YsP_vL3m-BPu5ePPMH8WIHulr3XgKPe-tBzsd_HOA1J1d8cIr4V9V6XPZ4oMWzgnD-aduAtw8vGZwhsDuKal3jOpkgPR0cTKPKz11ZDm7j9qXQ/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-1009 http://secure-web.cisco.com/1lvgi1uPw3Nu-oamZ02i-Yi0qZ3AZLrnrYrD6HIGWb0s4cAfOOd8T9uDv_cJULOkCeoT_HLEZQ53gmGQzZgul9-eiYfbcByWM3CBD2Zf50VCHIbm2tEhp_77Xn0aVkHwIfjzIcSwMdEZDlVv-CdgriXWS1rVV-BNJkIULn1JAvVCI7AptKu9VwwiLOea2UZ3ptnvIwBqSndw7uLOwnWayvQ4BKd1YqL71BsI-_8Cwi0F7-msFJdNPPGNOEiM_ja24J0oyXZYAdeqI0JuqUoeEyMN0F1S6r-2YyUaHhbFeUAxgdtHVWzT-786kn5T5kdjPfqE0DYqPa9E92FTusDrt6Q/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-1009
mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz http://secure-web.cisco.com/1s15sGfI9BvOll21Vf7Lbr8ewt_a4YUkQ6IXkTn9bJsAIk7sx-twNLmRPtM1ONZdCPtlO_hY8UEC435KH7GU-79gsiSG53ruzBX_5NlrmFXOePye6wFbs9fvlVdATLvOA1SQ0iqcuKBUbODGWU-fHEJTk9QiicutW3th2YjQsXrpmqioYeRxfdGWZkxxp9LU7vv9LweDmv93hNcAVXWJeNFH7zUfKBKr75nmPUyIRvjoy6XgVJIhF7-WVJvwcOwJ7FwLhZoDDcqnqOe4PTUkTcgBNpS6-s6PibffWmWsdl0o6LoRcRHs8Bg1TZRaju8Tla40E3o-_yPrVFMyKnhFfxg/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-1009%2Fmri%2Forig%2F001.mgz
mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-1009/ses-01/anat/sub-1009_ses-01_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-1009/mri/orig/001.mgz http://secure-web.cisco.com/1s15sGfI9BvOll21Vf7Lbr8ewt_a4YUkQ6IXkTn9bJsAIk7sx-twNLmRPtM1ONZdCPtlO_hY8UEC435KH7GU-79gsiSG53ruzBX_5NlrmFXOePye6wFbs9fvlVdATLvOA1SQ0iqcuKBUbODGWU-fHEJTk9QiicutW3th2YjQsXrpmqioYeRxfdGWZkxxp9LU7vv9LweDmv93hNcAVXWJeNFH7zUfKBKr75nmPUyIRvjoy6XgVJIhF7-WVJvwcOwJ7FwLhZoDDcqnqOe4PTUkTcgBNpS6-s6PibffWmWsdl0o6LoRcRHs8Bg1TZRaju8Tla40E3o-_yPrVFMyKnhFfxg/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-1009%2Fmri%2Forig%2F001.mgz
mri_convert: can't determine type of output volume Command exited with non-zero status 1 @#@FSTIME 2025:07:02:11:36:49 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 100% M 6144 F 0 R 270 W 0 c 0 w 2 I 0 O 0 L 0.30 0.56 0.42 @#@FSLOADPOST 2025:07:02:11:36:49 mri_convert N 2 0.30 0.56 0.42 Linux CLA19571.tu.temple.edu http://secure-web.cisco.com/1KjMhilgbPgI1ewd6dc-xXVQOGsJEbrGHz_GGegclf7cbDZYz4by_iJTwIbIKlJRghYUhGynnaVNe7wYyIH0ojoyouXcp3UKYqnQJgn7LlLmP-MRa6akR4Y4nWwzCL0NR_A4__GHOWnHTG51ogXI7-memKhTQliPXFj0Crz-e1bpIuvu3J497rRwl9HK20x6BqSP5dw6ifwX_vvODFKRLJXEtoUUfVa7nhq3kSMG3YsP_vL3m-BPu5ePPMH8WIHulr3XgKPe-tBzsd_HOA1J1d8cIr4V9V6XPZ4oMWzgnD-aduAtw8vGZwhsDuKal3jOpkgPR0cTKPKz11ZDm7j9qXQ/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-1009 exited with ERRORS at Wed Jul 2 11:36:49 EDT 2025
For more details, see the log file /home/tur31606@tu.temple.edu/freesurfer_output/sub-1009/scripts/recon-all.log http://secure-web.cisco.com/1t9ZwVUeAdhNGJIVhkSwplRHk8r86Lub0upqCHVfvH8ozIFhXNh8t7y0VuaecbY0-WlRVfPH0B1pXEpAV8-oNUp5h98UA4ZihL_uljKaMowOxcZ9SraZ-0j29UBhdSKioqQNqVkkdnbrLbMne2Ncge8Ivx37wnYmGgt4wLwg6upf0ROhVRlankabUOd1SHqB3KcA6Dv1dfok1-R2jLxcPbux-PN4hFq-I7B2fFZGLz3MGUV80jkmIPBM-fpM0ePRfptRldRQeJtwXkrZkAV2HKjykou7b7jQJdujZ9eiq8xAkib_jPLNoUMIO9OkbYAkavrG8tHS3T72ha4L7Z3lNBQ/http%3A%2F%2Ftur31606%40tu.temple.edu%2Ffreesurfer_output%2Fsub-1009%2Fscripts%2Frecon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://secure-web.cisco.com/1lZL5fd1-LIJV20MkpYIehpHZ9KjK6NT_O2y2M8boj9gcNFl_NiWxTbpk2_4C0Qz3hPiLQzV29FHHReSkcBJhCAhzH8xx5UJZHqGj9CV4hLE4XFYMZvF22Gwfl9_VP4pyuNVePSg-MLhJsxXp2k4xePZOej8_C5tkjTo6nML4aPtEctbIEYrBU9MZQQpGALr4taHlp1gl0sp8EZxIUbEl-uQ4XmZDWRNcNj_nrmbMFjS22ovWgYFgmdafMqAH4CmMpw8YVBmSOI1ZmRlWhLImZhliN42s72bO7vDbcEiXCtRqdSShoPQlmGwXYqXIA4D_zCNyRIL3qY5JSuAv-M9JoQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
Best, Andrew Cardona
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andrew cardona -
Douglas N. Greve