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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
http://secure-web.cisco.com/1-c9fAU-mJQQ9DmeM_Gnlo18O_sFsxXZw9Ukeytrvl0f-DQJ3POeaofW3DmjvyOSpco7-G1nRp5e0ngfwkeXeHALbht-WNDccVAs7b4raeXaDsZU0JlSXSwCnsg4W9zBPc1H4vCXgaBjnrbub9IMR2UhB0_5Q1AO4NprAYnsUiFf9A4_4xkRBILGJhkSW0Qjh3pg2dWxpGmR1ZCMud5nDjF9BoI8H8qF_D-ocw5EvoYhWFVGCPhloKJ9TdFccHkySHKw3-w1lJ5kbNMF8dcGtA18l2YvGrqHqZYIfFObH2WAiD9yIf-GWva06qHrO1rPLqDHAdw8_o6hRaVtSsb-hrA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<https://secure-web.cisco.com/1kgQgSn0M-wBXt5IMShtOiVREFkaVptte7zDgVLYmv5xFjaK1f9lQXuDQE1_vGxhsC4TrUgLCJj0Zix8yB1dpqOaCcRGwaTRKTMZbpziLMUZoYV-MAqO813l28x_OwrVizjPuTXO1Tu9rE1XnVSDlbsJyVlC8Ys-6yargDlnkdVbttP1MpQJ-8ZnvuNmZooCkLQWQHkPLKk3A4-toe0VMQwqL1TcfLPfOCvoJtkk_mmx10P7lcIK9-nS4sMv-0nBquvjc2tAKJ_VutoX4URBF1OebIGnycoeJNLN1GbRp3pyGPS2j9HcOqJaCwQK6Bog7kuNkV3U585XXrKuXvzmaHQ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!Mih3wA!HJEJdsO4S_WJryUpRE0_FRMLkASoTWM3q-5t4oLAMLC8aVWUeuH414z1f1kA02oCvEoNwud8Tm7UQ1bAygeEs0JZMyk$>
--
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
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