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.edu mailto:mreuter@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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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