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. > >
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU *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.