17 Sep
2014
17 Sep
'14
10:33 a.m.
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
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