Hi Martin，
I tried 2 times again (run 4 analysis at the same time). This time, it works well, The link to fsaverage is automatically created. I did not replicate the error message.
Thank you so much!
Best,
Jinsong
On Fri, Jul 29, 2016 at 11:44 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu
wrote:
Hi Jinsong,
can you give an example of what exactly does not work.
Thanks, Martin
On 07/29/2016 12:26 PM, Jinsong Tang wrote:
Hi Martin,
I checked all data are completed except the link to fsaverage, lh.EC_average and rh.EC_average. I run one analysis from the terminal. it works. if I run multiple analysis at the same time, it failed. When I manually linked the 3 files, then run multiple analysis at the same time, it works good.
Best,
Jinsong
On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
Hi Jinsong,
maybe not everything was copied? The link to fsaverage should be automatically created if it is missing. I often process cross in a different directory from base and long (and create symlinks to the cross subject dirs). It automatically creates fsaverage then. Try to replicate your problem with a single subject that failed. First try to do everything on the same computer, then try to do what you did before (copying parts of it).
Best, Martin
On 07/20/2016 12:56 PM, Jinsong Tang wrote:
Hi Martin,
We run all cross, base and long with 5.3. I guess the problem maybe we run cross on a computer and then copy the results to another computer to run the cross and long. the "*fsaverage" is not copied. Does this matter？*
Best，
Jinsong
On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter < mreuter@nmr.mgh.harvard.edumreuter@nmr.mgh.harvard.edu> wrote:
Hi Jinsong,
I have never seen this. Stable 5.3 is very stable and I doubt it is a bug. How did you process base and cross sectionals? Also with 5.3 ?
I would recommend to process cross and base with 5.3, then re-run the long and see if you can replicate this problem. Let me know what happens.
Best, Martin
On Jul 20, 2016, at 12:48 AM, Jinsong Tang < tangjinsonghn@gmail.com
tangjinsonghn@gmail.com> wrote:
Hi all,
I found an error during the longitudinal -long stream:
recon-all -long P1001-2 P1001 -all ......
FREESURFER_HOME /space/raid/fmri/freesurfer Actual FREESURFER_HOME /space/raid/fmri/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21
UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
......
mris_spherical_average -erode 1 -orig white -t 0.4 -o
P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject P1001-2.long.P1001. processing subject lh.EC_average...
MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg): could not open file
eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file
/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
Not a directory Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21
UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul 8
21:33:02 PDT 2016
Please help me fix this error!
Thanks and best regards,
Jinsong
<recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jinsong Tang, MD Institute of Mental Health The Second Xiangya Hospital , Central South University 139 Renmin Road, Changsha Hunan 410011, P.R. China
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.