Re: [Freesurfer] (no subject)

What happens if you try to run mri_convert ?

On 01/14/2016 05:10 PM, Jasmin Alves wrote:

Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l $FREESURFER_HOME/bin/tksurfer

-rwxr-xr-x 1 root wheel 103 May 14 2013 /Applications/freesurfer/bin/tksurfer

Jasmins-MacBook-Pro:freesurfer jasminalves$ $> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red

-bash: freeview: Permission denied

On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Jasmin, can you just cut and paste it into the email?

On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> Here is the output to the ls command
>
> On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves <jalves@usc.edu
<mailto:jalves@usc.edu>
> <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>> wrote:
>
>     Hi Dr. Greve,
>
>     I am still receiving the same message that I am denied access to
>     freeview. Is there anything I can do?
>
>     Thanks,
>     Jasmin
>
>     On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
>     <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>         Hi Jasmin, do you have permission to execute FS
commands? What
>         is the
>         result of
>         ls -l $FREESURFER_HOME/bin/tksurfer
>
>
>
>         On 01/14/2016 04:16 PM, Jasmin Alves wrote:
>         > Hello,
>         >
>         > I recently downloaded freesurfer on my mac with a Yosemite
>         operating
>         > system. The application itself appears to work,
however I am
>         not able
>         > to use the command line to do any of the testing free
surfer
>         commands,
>         > as I keep getting a access denied. I have attached a
>         screenshot. Your
>         > help would be very useful.
>         >
>         > Thank you,
>         > Jasmin
>         >
>         > --
>         > Jasmin Alves
>         > Predoctoral Student
>         > Medical Biology Graduate Program
>         > University of Southern California
>         > jalves@usc.edu <mailto:jalves@usc.edu>
<mailto:jalves@usc.edu <mailto:jalves@usc.edu>>
>         <mailto:jalves@usc.edu <mailto:jalves@usc.edu>
<mailto:jalves@usc.edu <mailto:jalves@usc.edu>>>
>         >
>         >
>         >
>         > _______________________________________________
>         > 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
>
>         --
>         Douglas N. Greve, Ph.D.
>         MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>         Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
>         Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
>
>         Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>         <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>         FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>       
 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>         Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>  _______________________________________________
>         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.
>
>
>
>
>     --
>     Jasmin Alves
>     Predoctoral Student
>     Medical Biology Graduate Program
>     University of Southern California
> jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
<mailto:jalves@usc.edu>>
>
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
<mailto:jalves@usc.edu>>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu

---

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