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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/1-76aEy05df7D8YaI6eF1TTSi7PfbpgqGmxvrpopTG6UzZ7P...
--
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HiAV9lBi1iMxMH3MhVMXWab6BUBnO-Q74GyygNnfL784hW...https://secure-web.cisco.com/1W2AK4NpQlQZJKbmrIXcmWCG4iMqWwnEGvj8VkOrgCEPolotXeMEBFzFMNtJ-xn72e95ZhXv-iGHHmg_jgKyh--iqyPMv3S3OiazpQUFCiJyGo08FtwSnTeCCgtBBkjvGyTVmBCdPWVCKx0KriQY7N25VZR-wZomAAAVILFLRRhytoTLfWCxCUbyHdzp60gOrqYXQ3h_2DiQHq5y4lD-PPa6Z_qwDOVaiavmICuzuVxcdVPNduVawiWRHFZRYQOnilDxd34Gqw0ziELtjTNISD0bHFWUbwMA0nGdKMA9DjSj5d0PSyhF8120_0YMvdMjqsLzYfxq2T8_JdNRJwWuL6Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!Mih3wA!EJhVthOAKBSXJV3VwfFE2qwKzHBa2NyOVckVgPuymsXDHIVXhZxC_C5IVfaFgmI9_ywI6d3gsw8eh1Y4vMP4z0o$
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 http://secure-web.cisco.com/1-c9fAU-mJQQ9DmeM_Gnlo18O_sFsxXZw9Ukeytrvl0f-DQJ...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-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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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:
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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-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
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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-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
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
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Dear FS team,
There was indeed a problem with recon-all and I reran the subject and did what you said, and now there is no mris_preproc read error. Thank you very much for your assistance!
All my best, 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 Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, June 9, 2022 1:27 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc read error
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Joanna L Eckhardt jeckhardt@health.ucsd.edumailto:jeckhardt@health.ucsd.edu Sent: Friday, June 3, 2022 10:37 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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://secure-web.cisco.com/1E2JEASEau2YgVC1uYGS1ZsM_9oqtVWK-luYnJ-DRUJMLTeA...https://secure-web.cisco.com/1Th0PZXn1coXyIACHhEcgcyj1fx0EuhNPWDosofr_MJJTQ30UDkchTWeBVIpuZ7VYrDcVrpcveffwJqskyhtvLsTdp_-tojBti6kDtP6FRb-TLlG-tB2vXIvySGv32BcXrBaSJ4zX_WIrbKxXqecEQOBDZA2gWkuBcWVULOeVSqc1pUScUW0PHT3JBYREK-lVU9v0pdn9TAWBUbSfInJ7Eoqu3X0Z5xDURxXANQYwkiuJz7XxKaRbFPvlqsQ4kUvRt1eAsu80Zn5TI_-hhwBqENbl8fVII90NHn_GamrPGKz180rK43mzpZe1PLzbypwyQlyno9a5UCeaWXcL6ixfzQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1ssWwnSJdU0eQ-n786E-FcmKzMDbsVTfydbWCV-aMnNsdHnXIySmZ6ne6JHLrI4OnJHJzddPtWfAR8VrZCsrM0yG89MPou0Q7Ak69BT32T8yOLv8f3vT212Osp4bVMMna3QmIY6peDq8TRA9hzedc5DBazeogxbwzbl89NKUeCh4XIDV2vrgTmUhQ9yOXhx-f9BhIa0aqYvRPuQLaQrx7eeCHTuC6_opG3NUwp9mUMcvuCP1pX7H2sUWdgQv1ZiqVl-X2RF3dC9ochRMfarPDlfxo0MZ4PSZGaulNSrsS6je-zz4vvS27658zC7wy1L2uE-3r8CyjLQGYFDcuuLxjSQ%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21Mih3wA*21HJEJdsO4S_WJryUpRE0_FRMLkASoTWM3q-5t4oLAMLC8aVWUeuH414z1f1kA02oCvEoNwud8Tm7UQ1bAygeEs0JZMyk*24__;JSUlJSUlJSUlJSUlJSUl!!Mih3wA!EDLRDz_ukzpNNMI9vNp3j8TtG5u1PLntHPZlfnyZMgSOD3YrEfEj34NEgox2xQuNwwO_uXecvMOM7flIh1gKPVM$
--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, June 3, 2022 10:03 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Joanna L Eckhardt