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 <mreu...@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 < > mreu...@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 < >> <mreu...@nmr.mgh.harvard.edu>mreu...@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 < <tangjinson...@gmail.com> >>> tangjinson...@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 >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@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 > listfreesur...@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 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.
