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
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
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.
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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
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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
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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
Hmm. Well I'm stumped. Sorry. :-/
Any Freesurfer gurus have some ideas here?
On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud zeydabadi@gmail.com wrote:
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 > > > _______________________________________________ > 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. > >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
Paul,
I am using bash instead of tcsh. Does it make any difference ?
Mahmoud
On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach pabeach1@gmail.com wrote:
Hmm. Well I'm stumped. Sorry. :-/
Any Freesurfer gurus have some ideas here?
On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud zeydabadi@gmail.com wrote:
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 >> >> >> _______________________________________________ >> 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. >> >> > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > _______________________________________________ > 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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
No it doesnt make a difference.
Are you using a the virtual machine version of freesurfer with a shared folder? Or some other system where you are mounting a readonly file system? That is most likely your issue.
You will have to place your subjects directory onto a location in which you have write permissions.
-Zeke
On 09/17/2014 10:16 AM, Mahmoud wrote:
Paul,
I am using bash instead of tcsh. Does it make any difference ?
Mahmoud
On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com mailto:pabeach1@gmail.com> wrote:
Hmm. Well I'm stumped. Sorry. :-/ Any Freesurfer gurus have some ideas here? On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>> wrote: 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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Zeke,
I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and Windows 7-64 as host. I made a shared directory between windows and Ubuntu named DBSI where then I put the /volumetric/MGZ under it. So, how can I give permission for that ?
Mahmoud
On Wed, Sep 17, 2014 at 10:21 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
No it doesnt make a difference.
Are you using a the virtual machine version of freesurfer with a shared folder? Or some other system where you are mounting a readonly file system? That is most likely your issue.
You will have to place your subjects directory onto a location in which you have write permissions.
-Zeke
On 09/17/2014 10:16 AM, Mahmoud wrote:
Paul,
I am using bash instead of tcsh. Does it make any difference ?
Mahmoud
On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com mailto:pabeach1@gmail.com> wrote:
Hmm. Well I'm stumped. Sorry. :-/ Any Freesurfer gurus have some ideas here? On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>> wrote: 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:zeydabadi@gmail.com>> wrote: Dear All, I ran the following script: #!/bin/bashSUBJECTS_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, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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The information in this e-mail is intended only for the person to whom itis
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 HelpLineat
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 *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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I dont know all the details regarding shared directories between the host and guest, but the bottom line is that if you can not manually create a symbolic link in the subjects dir than you will not be able to run recon-all.
Another option is to use the shared directory to copy the subjects dir into the file system in virtual machine space.
-Zeke
On 09/17/2014 10:33 AM, Mahmoud wrote:
Zeke,
I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and Windows 7-64 as host. I made a shared directory between windows and Ubuntu named DBSI where then I put the /volumetric/MGZ under it. So, how can I give permission for that ?
Mahmoud
On Wed, Sep 17, 2014 at 10:21 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
No it doesnt make a difference. Are you using a the virtual machine version of freesurfer with a shared folder? Or some other system where you are mounting a readonly file system? That is most likely your issue. You will have to place your subjects directory onto a location in which you have write permissions. -Zeke On 09/17/2014 10:16 AM, Mahmoud wrote: > Paul, > > I am using bash instead of tcsh. Does it make any difference ? > > Mahmoud > > On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com> > <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote: > > Hmm. Well I'm stumped. Sorry. :-/ > > Any Freesurfer gurus have some ideas here? > > On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com> > <mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>> wrote: > > 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 <mailto:pabeach1@gmail.com> > <mailto:pabeach1@gmail.com <mailto: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 <mailto:zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com <mailto: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 <mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto: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 <mailto:zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com <mailto: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 <mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto: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 <mailto:zeydabadi@gmail.com> > <mailto:zeydabadi@gmail.com <mailto: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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric > *N*eurology *T*eam (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology > *T*eam (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam > (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Sep 17, 2014 at 11:05 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
I dont know all the details regarding shared directories between the host and guest, but the bottom line is that if you can not manually create a symbolic link in the subjects dir than you will not be able to run recon-all.
Another option is to use the shared directory to copy the subjects dir into the file system in virtual machine space.
-Zeke
On 09/17/2014 10:33 AM, Mahmoud wrote:
Zeke,
I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and Windows 7-64 as host. I made a shared directory between windows and Ubuntu named DBSI where then I put the /volumetric/MGZ under it. So, how can I give permission for that ?
Mahmoud
On Wed, Sep 17, 2014 at 10:21 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
No it doesnt make a difference. Are you using a the virtual machine version of freesurfer with ashared
folder? Or some other system where you are mounting a readonly file system? That is most likely your issue. You will have to place your subjects directory onto a location inwhich
you have write permissions. -Zeke On 09/17/2014 10:16 AM, Mahmoud wrote: > Paul, > > I am using bash instead of tcsh. Does it make any difference ? > > Mahmoud > > On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote: > > Hmm. Well I'm stumped. Sorry. :-/ > > Any Freesurfer gurus have some ideas here? > > On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>>wrote:
> > 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 mailto:pabeach1@gmail.com
> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>>wrote:
> > you have to tell the symbolic link where to put thedirectory
> > copy this exactly into your terminal, including theperiod
> 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 <mailto:zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com <mailto: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 <mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote: > > Try something like: > > cd $SUBJECTS_DIR > ln -s $FREESURFER_HOME/subjects/fsaverage . > > Confirm the linked directory is now in your > $SUBJECTS_DIR, then try running your script. > > On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud > <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>> > wrote: > > Paul, > > The fsaverages are in$FREESURFER_HOME/subjects.
> So does it mean that the program couldn'tmake a
> link between my actual image places and > $FREESURFER_HOME/subjects/fsaverage ? > what can I do to fix it ? > > Thank you, > Mahmoud > > On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach > <pabeach1@gmail.com <mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> > wrote: > > The general fsaverage (as well as it'sother
> iterations, fsaverages 3-6) should be > located in your$FREESURFER_HOME/subjects
> directory. You could symbolically linkit
> over to your $SUBJECTS_DIR. > > On Wed, Sep 17, 2014 at 9:09 AM,Mahmoud
> <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>
> <mailto:zeydabadi@gmail.com <mailto: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 knowhow 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 1619:26:47 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 symboliclink
> './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 openlabel
> 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_64GNU/Linux
> > recon-all -s case022_tp2 exitedwith
> 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 towhom it is
> addressed. If you believe this> was sent to you in error and the> contains patient information,please
> contact the Partners ComplianceHelpLine at
>http://www.partners.org/complianceline . > If the e-mail was sent to you inerror
> but does not contain patient > information, please contact thesender
> and properly > dispose of the e-mail. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric > *N*eurology *T*eam (*CoGeNT*) > >
> Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail isintended
> only for the person to whom it is > addressed. If you believe this e-mailwas
> sent to you in error and the e-mail > contains patient information, pleasecontact
> the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If > the e-mail was sent to you in error > but does not contain patientinformation,
> please contact the sender and properly > dispose of the e-mail. > > > >
> Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intendedonly
> for the person to whom it is > addressed. If you believe this e-mail wassent
> to you in error and the e-mail > contains patient information, pleasecontact 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 *Co*gnitive and *Ge*riatric*N*eurology
> *T*eam (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intendedonly for
> the person to whom it is > addressed. If you believe this e-mail was sentto
> you in error and the e-mail > contains patient information, please contactthe
> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended onlyfor the
> person to whom it is > addressed. If you believe this e-mail was sent toyou 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, pleasecontact
> 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 *Co*gnitive and *Ge*riatric *N*eurology *T*eam > (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> error and the e-mail > contains patient information, please contact thePartners
> Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, pleasecontact the
> sender and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for theperson
> to whom it is > addressed. If you believe this e-mail was sent to you inerror
> 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 contactthe
> 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 *Co*gnitive and *Ge*riatric *N*eurology *T*eam(*CoGeNT*)
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 personto
> whom it is > addressed. If you believe this e-mail was sent to you in errorand
> the e-mail > contains patient information, please contact the PartnersCompliance
> 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 thesender
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yeah, I was starting to wonder if he was having permissions issues as well.
On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud zeydabadi@gmail.com wrote:
Paul,
I am using bash instead of tcsh. Does it make any difference ?
Mahmoud
On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach pabeach1@gmail.com wrote:
Hmm. Well I'm stumped. Sorry. :-/
Any Freesurfer gurus have some ideas here?
On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud zeydabadi@gmail.com wrote:
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 >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) >> >> _______________________________________________ >> 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. > >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
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@nmr.mgh.harvard.edu