No errors yet, still going and went pretty fast, not finish yet.
and no fsavg is not a symbolic link.
thanks.
On Mon, Jul 29, 2013 at 1:52 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
You are getting the same error as before? Could you send the log/terminal output?
Are the folders in fsavg symlinks also?
On Mon, 29 Jul 2013, Pom Sailasuta wrote:
So now I got the following in /home/pom/Software/freesurfer/**subjects
dir and still no lh.BA1.label per your first email.
[pom@PomLinux /home/pom/Software/freesurfer/**subjects]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-29 10:39 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.**tar.gz lrwxrwxrwx 1 pom pom 17 2013-07-29 10:39 fsaverage -> ./fsavg/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit
On Mon, Jul 29, 2013 at 1:37 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote: ok, that's good. Just make a symlink to the fsaverage dir from your subjects dir (/home/pom/Software/**freesurfer/subjects)
i.e. cd /home/pom/Software/freesurfer/**subjects ln -s ./fsavg/fsaverage . -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: fsavg dir contains several directories. [pom@PomLinux /home/pom]% cd fsavg [pom@PomLinux /home/pom]% ls fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6lh.EC_average rh.EC_average V1_average
thanks again. On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote: what is fsavg in that same directory? Maybe fsaveragewas renamed to fsavg?
You would just need to copy the fsaverage recon folderback into /home/pom/Software/freesurfer/**subjects, no need to reinstall. -Louis
On Mon, 29 Jul 2013, Pom Sailasuta wrote: hi, yes, but it is a link, not sure how is thishappen.
//////////////////////////////**///// [pom@PomLinux /home/pom]% pwd /home/pom/Software/freesurfer/**subjects [pom@PomLinux /home/pom]% ls -al total 10981644 drwxr-xr-x 9 pom pom 4096 2013-07-2907:24 . drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 buckner_data-tutorial_subjs.**tar.gz lrwxrwxrwx 1 pom pom 48 2013-07-29 07:24 fsaverage -> /home/pom/Software/freesurfer/** subjects/fsaverage drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit //////////////////////////////**///////////////
I think it linked to itself, should I re-installfreesurfer.
thanks Pom On Mon, Jul 29, 2013 at 1:09 PM, Louis NicholasVinke vinke@nmr.mgh.harvard.edu wrote: Hi Pom, Does the following path exist? /home/pom/Software/freesurfer/** subjects/fsaverage/label/
if so, do it contain lh.BA1.label? Itprobably has something do with the fsaverage symbolic link. A few lines up in your error log it prints "Too many levels of symbolic links". -Louis
On Mon, 29 Jul 2013, Pom Sailasuta wrote: Hi, I am wondering the errors I got fromrecon-all is from my FreeSurfer installation, please comments.
Here is my error: //////////////////////// Reporting on 70 segmentations /home/pom/Software/freesurfer/**subjects/S009002A/label #-----------------------------**
#@# BA Labels lh Mon Jul 29 07:24:35PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...
cd /home/pom/Software/freesurfer/**subjects;ln -s /home/pom/Software/freesurfer/** subjects/fsaverage; cd -
mri_label2label --srcsubjectfsaverage --srclabel
/home/pom/Software/freesurfer/**subjects/fsaverage/label/lh.**BA1.label --trgsubject S009002A --trglabel ./lh.BA1.label --hemi lh --regmethod surface
Too many levels of symbolic links mri_label2label: could not open labelfile
/home/pom/Software/freesurfer/**subjects/fsaverage/label/lh.**BA1.label
srclabel = /home/pom/Software/freesurfer/**subjects/fsaverage/label/lh.**BA1.label srcsubject = fsaverage trgsubject = S009002A trglabel = ./lh.BA1.label regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/pom/Software/freesurfer/**subjects FREESURFER_HOME/home/pom/Software/freesurfer Loading source label. Invalid argument ERROR reading
/home/pom/Software/freesurfer/**subjects/fsaverage/label/lh.**BA1.label Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 21:36:53 UTC 2013 i686 GNU/Linux
recon-all -s S009002A exited withERRORS at Mon Jul 29 07:24:35 PDT 2013
For more details, see the log file /home/pom/Software/freesurfer/**subjects/S009002A/scripts/**recon-all.log To report a problem, see
http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> ////////////////////////////// thanks Pom The information in this e-mail is intended onlyfor 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/**compliancelinehttp://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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