the easiest thing to do is:
cd /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage
then you don't have to worry about source and target. It will implicitly
create the symlink in $PWD
cheers
Bruce
On Fri, 19 Sep
2014, Mahmoud
wrote:
Bruce,
By "symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
/mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage" ?
which fsaverage is the target ?
Thanks,
Mahmoud
On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud <[email protected]> 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
<[email protected]> 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
<[email protected]>
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
<[email protected]>
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
<[email protected]>
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
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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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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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[email protected]
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.
