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.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> 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
>
>

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_______________________________________________
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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.
_______________________________________________
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-- 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