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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Joanna L Eckhardt <jeckhardt@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


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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

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