On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud <zeydabadi@gmail.com> wrote:

Bruce,

Thank you for your follow up and advice. Please let me know:
1- How to download the fsaverage again?
2- should I do the symlink manually or it will be done by recon-all later ?
3- What steps should I take before running the recon-all -all ? should I create any specific directory? set any permission ?

Best,
Mahmoud

On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
yes, you symlinked it to itself which is why you are getting the infinite recursion error. You need to delete /usr/local/freesurfer/subjects/fsaverage

and download the fsaverage dir again, put it in that directory, then symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/subjects/fsaverage

cheers
Bruce
On Fri, 19 Sep 2014, Mahmoud wrote:

Bruce,

I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
permission error the same point that I got the symlink error lastly. So, I
tought that might be due to something related to shared directory.
Then I copied my subjects under the $SUBJECTS_DIR but got the symlink error.

running ls -l /usr/local/freesurfer/subjects /fsaverage shows me this:

lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
/usr/local/freesurfer/subjects/fsaverage ->
/usr/local/freesurfer/subjects/fsaverage

Thank you,
Mahmoud

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

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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.