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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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/tur31...@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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