On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

the directory /usr/local/freesurfer/subjects is for subjects that we distribute and NOT where you should be putting your subject data. Is that what you are doing? You may have overwritten the fsaverage dir there. Can you run:

ls -l /usr/local/freesurfer/subjects/fsaverage

and send us the results?

you should create a directory elsewhere with your subject data and point SUBJECTS_DIR at it

cheers
Bruce

On Fri, 19 Sep 2014, Mahmoud wrote:

Bruce,

Here is the info when I open a new terminal:

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
ubuntu:~>

On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
can you tell us what your FREESURFER_HOME is and what your
SUBJECTS_DIR is? You will need to remove the broken link
probably

On Fri, 19 Sep 2014, Mahmoud wrote:

Hi Bruce,

Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many
levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory under SUBJETCS_DIR
named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken
link, and I have no idea
why the the link is broken and how to fix it.
Any help would be highly appreciated !

Thank you,
Mahmoud

On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Mahmoud

were you able to create a symlink to fsaverage
in your
SUBJECTS_DIR? If not, that is the reason for
this error
Bruce

On Thu, 18 Sep 2014, Mahmoud wrote:

Dear all,

After running "recon-all -i

$SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
-subject case018_tp2 -all" I'm always
getting the
following error and really
don't know how to fix.

Could anybody please help me. The
recon-all.log file
is attached.

Thank you,
Mahmoud

Reporting on 70 segmentations
mri_segstats done

/usr/local/freesurfer/subjects/case018_tp2/label

#--------------------------------------------
#@# BA Labels lh Thu Sep 18 20:23:27 EDT
2014
INFO: fsaverage subject does not exist
in
SUBJECTS_DIR
INFO: Creating symlink to fsaverage
subject...

cd /usr/local/freesurfer/subjects; ln
-s

/usr/local/freesurfer/subjects/fsaverage; cd -

mri_label2label --srcsubject fsaverage
--srclabel

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
--trgsubject
case018_tp2 --trglabel ./lh.BA1.label
--hemi lh
--regmethod surface

Too many levels of symbolic links
mri_label2label: could not open label
file

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

srclabel =

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = case018_tp2
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
/usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
Linux ubuntu 3.13.0-35-generic
#62-Ubuntu SMP Fri
Aug 15 01:58:42 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s case018_tp2 exited with
ERRORS at Thu
Sep 18 20:23:27 EDT 2014

For more details, see the log file

/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

_______________________________________________
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 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 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.