17 Sep
2014
17 Sep
'14
11:05 a.m.
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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