Paul

it shows again:
ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

!!!

On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach <pabeach1@gmail.com> wrote:

you have to tell the symbolic link where to put the directory

copy this exactly into your terminal, including the period at the end

SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ

cd $SUBJECTS_DIR

ln -s $FREESURFER_HOME/subjects/fsaverage .

On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud <zeydabadi@gmail.com> wrote:

Paul,

I tried this:
SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage

and got this:
ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

any idea ?

Mahmoud

On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach <pabeach1@gmail.com> wrote:

Try something like:

cd $SUBJECTS_DIR

ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud <zeydabadi@gmail.com> wrote:

Paul,

The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage ? 

what can I do to fix it ?

Thank you,

Mahmoud

On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach <pabeach1@gmail.com> wrote:

The general fsaverage (as well as it's other iterations, fsaverages 3-6) should be located in your $FREESURFER_HOME/subjects directory. You could symbolically link it over to your $SUBJECTS_DIR.

On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud <zeydabadi@gmail.com> wrote:

Dear All,

I ran the following script:

#!/bin/bash
SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all

and got the error below at the end. Could anybody please let me know how to fix it.

Thank you,

Mahmoud

Reporting on  70 segmentations
mri_segstats done
/mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
#--------------------------------------------
#@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s /usr/local/freesurfer/subjects/fsaverage; cd -

ln: failed to create symbolic link './fsaverage': Operation not supported

 mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface

No such file or directory
mri_label2label: could not open label file /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label

srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = case022_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    /mnt/hgfs/DBSI/volumetric/MGZ
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014

For more details, see the log file /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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--

Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program

 - MSU Cognitive and Geriatric Neurology Team (CoGeNT)

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The information in this e-mail is intended only for the person to whom it is
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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
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

--

Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program

 - MSU Cognitive and Geriatric Neurology Team (CoGeNT)

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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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.