Try something like:cd $SUBJECTS_DIRln -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,MahmoudOn 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:_______________________________________________MahmoudThank you,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.
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
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.
--Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program- MSU Cognitive and Geriatric Neurology Team (CoGeNT)
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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.