It looks like something might have gone wrong during recon-all for that
subject. Does recon-all.log say it completed successfully? Try deleting
the lh.sphere.reg (and any other file with 0 size) and running recon-all
-autorecon2-surfonly -autorecon3, then do -qcache
On 6/7/2022 12:41 PM, Joanna L Eckhardt wrote:
External Email - Use Caution
Dear FS team,
I am emailing to check in on the status of this issue. Any insights on
how to move forward with this error? I can try rerunning this subject
in the meantime to see if that fixes the problem.
Thank you very much your assistance!
Best wishes,
Joanna
*--*
*Joanna Eckhardt***
Neurosciences Graduate Program
University of California, San Diego
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Joanna L
Eckhardt <jeckha...@health.ucsd.edu>
*Sent:* Friday, June 3, 2022 10:37 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_preproc read error
External Email - Use Caution
Dear FreeSurfer team,
I reran -qcache for sub-101 (also, I had specified -qcache processing
for all subjects during initial recon-all so it /should/ have already
occurred), and it exited with errors. Below is the output from the
-qcache rerun, with the error being:
ERROR: reading
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1
Let me know if you have any insights, or if I need to rerun the
recon-all for this subject.
Thank you for your assistance!
Joanna
*developer@developer-VirtualBox*:*~/FreeSurfer/osg-outputs/cannabis-BL*$
recon-all -s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun 3 13:28
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
Update not needed
#@# white area lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
Update not needed
#@# pial curv lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
Update not needed
#@# pial area lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
Update not needed
#@# thickness lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
Update not needed
#@# area and vertex vol lh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
../surf/lh.thickness
Update not needed
#@# white curv rh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
Update not needed
#@# white area rh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Update not needed
#@# pial curv rh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
Update not needed
#@# pial area rh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
Update not needed
#@# thickness rh Fri Jun 3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
Update not needed
#@# area and vertex vol rh Fri Jun 3 13:29:48 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
../surf/rh.thickness
Update not needed
#--------------------------------------------
#@# Qdec Cache preproc lh thickness fsaverage Fri Jun 3 13:29:48 EDT 2022
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf
mris_preproc --s sub-101 --hemi lh --meas thickness --target fsaverage --out
lh.thickness.fsaverage.mgh
nsubjects = 1
tmpdir is ./tmp.mris_preproc.3286
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf
Log file is lh.thickness.fsaverage.mris_preproc.log
Fri Jun 3 13:29:48 EDT 2022
setenv SUBJECTS_DIR /home/developer/FreeSurfer/osg-outputs/cannabis-BL
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf
/usr/local/freesurfer/7.2.0/bin/mris_preproc --s sub-101 --hemi lh --meas
thickness --target fsaverage --out lh.thickness.fsaverage.mgh
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
mris_preproc 7.2.0
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
tmpdir is ./tmp.mris_preproc.3286
Src lh sphere.reg
Trg lh sphere.reg
---------------------------------------------------
#@# 1/1 sub-101 Fri Jun 3 13:29:48 EDT 2022 --------------
-----------------------
mri_surf2surf --srcsubject sub-101 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval
./tmp.mris_preproc.3286/sub-101.1.mgh --sval
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness
--sfmt curv --noreshape --cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
7.2.0
setenv SUBJECTS_DIR /home/developer/FreeSurfer/osg-outputs/cannabis-BL
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf
mri_surf2surf --srcsubject sub-101 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval
./tmp.mris_preproc.3286/sub-101.1.mgh --sval
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness
--sfmt curv --noreshape --cortex
sysname Linux
hostname developer-VirtualBox
machine x86_64
user developer
srcsubject = sub-101
srcval =
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness
srctype = curv
trgsubject = fsaverage
trgval = ./tmp.mris_preproc.3286/sub-101.1.mgh
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = lh.cortex.label
label-trg = lh.cortex.label
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
ERROR: reading
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1
@#@FSTIME 2022:06:03:13:29:48 mris_preproc N 10 e 0.09 S 0.01 U 0.07 P 92% M
6600 F 0 R 7976 W 0 c 69 w 146 I 0 O 8 L 0.00 0.00 0.08
@#@FSLOADPOST 2022:06:03:13:29:48 mris_preproc N 10 0.00 0.00 0.08
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-101 exited with ERRORS at Fri Jun 3 13:29:48 EDT 2022
For more details, see the log file
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
To report a problem, see*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <https://secure-web.cisco.com/1ssWwnSJdU0eQ-n786E-FcmKzMDbsVTfydbWCV-aMnNsdHnXIySmZ6ne6JHLrI4OnJHJzddPtWfAR8VrZCsrM0yG89MPou0Q7Ak69BT32T8yOLv8f3vT212Osp4bVMMna3QmIY6peDq8TRA9hzedc5DBazeogxbwzbl89NKUeCh4XIDV2vrgTmUhQ9yOXhx-f9BhIa0aqYvRPuQLaQrx7eeCHTuC6_opG3NUwp9mUMcvuCP1pX7H2sUWdgQv1ZiqVl-X2RF3dC9ochRMfarPDlfxo0MZ4PSZGaulNSrsS6je-zz4vvS27658zC7wy1L2uE-3r8CyjLQGYFDcuuLxjSQ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__%3B%21%21Mih3wA%21HJEJdsO4S_WJryUpRE0_FRMLkASoTWM3q-5t4oLAMLC8aVWUeuH414z1f1kA02oCvEoNwud8Tm7UQ1bAygeEs0JZMyk%24>
*--*
*Joanna Eckhardt***
Neurosciences Graduate Program
University of California, San Diego
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Friday, June 3, 2022 10:03 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_preproc read error
Try running recon-all -s subject -qcache for that subject
On 6/2/2022 7:55 PM, Joanna L Eckhardt wrote:
External Email - Use Caution
Dear FreeSurfer Help Team,
I am working through the FreeSurfer tutorial on cannabis using Ubuntu
VM on windows (FS version 7.1.1). I am on the group analysis portion
of the tutorial attempting to run mris_preproc. However, I am
receiving the following error upon running the script:
error: No such file or directory
error:
mghRead(/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/rh.thickness.fwhm10.fsaverage.mgh,
-1): read error
I wonder if something has been going wrong with recon-all as I
believe it is saying that there is an error with one of the outputs
in sub-101? Recon-all has been running in a suspiciously short time
(~5 hours), but I do not know enough about the processing steps to
know what might be occurring wrong in recon-all or in trying to run
mris_preproc.
Please let me know if I can send you anything else to provide more
information on the issue.
Thank you for your time and assistance.
Best wishes,
Joanna
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1JNnhKNa5W6PSrzjvnMkvIUBHWzitJmLLYr3rj9rgmnPCDImdJOdYmlAAdevnbF2OlzRQYrCdFyrlxYXp43aIYkAb6rDkcWTnYpW0PfUy5hUDMLocNn9cLP8WypXakReVr74tNOND3EkQncuXDlF98g2GT0nsX8yfQZ4qnBY9yt16KFyKHj3Eyfe1YDmyimHKBhsdIxqwZvFXwRQgrNhc7HPg0Cl3qBRNyc9MlwtjPLYl7gKtSsoZ0V2TNCl_02NaAzrqtq7YfAqam6f-f02skOH5iObMz684CypsULas8Gi9AFhfBDruWKnzppglBZgjV8VbUmn0fEVRP1AIiJeU8g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1PCFECN4Y_BugIvXsNoZOmNzKyL5MhQzeZfFLjEqiQ_2V3dKNriJVAMJa1JD0ENUxzZTfuISiKUq94IhiR_AARYs7IV2wKFqUqRDakK8Hps-N8nrmedCeQjCehtXy5ZKSeLboQ--5MZ-vwB8DckJf_6rAYsOtftGs2nelPPm9bzhGDIJm0uQX-K9gBHKrdwmTlb9xxuOYqS1n3scxl-6Gg_9eNaPCZv50kjqh_Fo0Xc6hQZAO-Y0dhOzJ0jOPFG5v6Ae9kFd37AFv7M2VaSFQCenRhziq3i6IttMre4t1GiNy3uGAGPQTRfc3poZKqOWY9r2SR1k_cb9jWTxOjAtJ8Q%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21Mih3wA%2A21EJhVthOAKBSXJV3VwfFE2qwKzHBa2NyOVckVgPuymsXDHIVXhZxC_C5IVfaFgmI9_ywI6d3gsw8eh1Y4vMP4z0o%2A24__%3BJSUlJSUlJSUlJSUlJSUlJQ%21%21Mih3wA%21HJEJdsO4S_WJryUpRE0_FRMLkASoTWM3q-5t4oLAMLC8aVWUeuH414z1f1kA02oCvEoNwud8Tm7UQ1bAygeEU0mnXCE%24>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
