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 <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@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 <pabea...@gmail.com > <mailto:pabea...@gmail.com> > > <mailto:pabea...@gmail.com <mailto:pabea...@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 <zeydab...@gmail.com > <mailto:zeydab...@gmail.com> > > <mailto:zeydab...@gmail.com <mailto:zeydab...@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 <pabea...@gmail.com > <mailto:pabea...@gmail.com> > > <mailto:pabea...@gmail.com <mailto:pabea...@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 > > <zeydab...@gmail.com <mailto:zeydab...@gmail.com> > <mailto:zeydab...@gmail.com <mailto:zeydab...@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 > > <pabea...@gmail.com <mailto:pabea...@gmail.com> > <mailto:pabea...@gmail.com <mailto:pabea...@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 > > <zeydab...@gmail.com > <mailto:zeydab...@gmail.com> <mailto:zeydab...@gmail.com > <mailto:zeydab...@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 > > <pabea...@gmail.com > <mailto:pabea...@gmail.com> <mailto:pabea...@gmail.com > <mailto:pabea...@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 > > <zeydab...@gmail.com > <mailto:zeydab...@gmail.com> > > <mailto:zeydab...@gmail.com > <mailto:zeydab...@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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
