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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Here is the output to the ls command
On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves 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> 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
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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
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> 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>> 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>> > > > > _______________________________________________ > 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 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>-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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> 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>>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>> > > > > _______________________________________________ > 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 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>-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jasmin,
Did you follow the instructions from the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall which links to this mac specific page. https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
?
hth d
On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves jalves@usc.edu 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 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> 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>>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>> > > > > _______________________________________________ > 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 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>-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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.
Yes I did. I was on the last step, the testing freesurfer when I discovered the commands do not work
On Thu, Jan 14, 2016 at 2:14 PM, dgw dgwakeman@gmail.com wrote:
Jasmin,
Did you follow the instructions from the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall which links to this mac specific page. https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
?
hth d
On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves jalves@usc.edu 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>
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> 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>>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>> > > > > _______________________________________________ > 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 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>-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That command seems to work; Here is the output. However in order to prevent the message "access denied" though, should I re-download freesurfer and make a new license text file?
EXAMPLE 1
APPLYING TRANSFORMS (INCLUDING TALAIRACH)
The volume can be resampled into another space by supplying a
transform using the --apply_transform flag. This reads the transform
file and applies the transform (when --apply_inverse_transform is
used, the transform is inverted and then applied). An example of a
transform file is talairach.xfm as found in subjectid/mri/transforms.
To convert a subject's orig volume to talairach space, execute the
following lines:
* cd subjectid/mri mkdir talairach mri_convert --apply_transform
transforms/talariach.xfm --devolvexfm subjectid --ic 0 0 0 orig
talairach
This properly accounts for the case where the input volume does not
have it's coordinate center at 0.To evaluate the result, run:
* tkmedit -f $SUBJECTS_DIR/talairach/mri/orig -aux talairach
The main and aux volumes should overlap very closely. If they do not,
use tkregister2 to fix it (run tkregister --help for docs).
EXAMPLE 2
From the subject directory: mri_convert -at mri/transforms/talairach_
one.m3z mri/norm.mgz mri/norm_transformed_by_gca_one.mgz
BUGS
None
REPORTING
Report bugs to freesurfer@nmr.mgh.harvard.edu
SEE ALSO
mris_convert
Jasmins-MacBook-Pro:subjects jasminalves$
On Fri, Jan 15, 2016 at 9:09 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 accessto
> 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 aYosemite
> 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 contactthe
> 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
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I have processed a subject through recon_all successfully. Then I pushed it through the full mri_cvs_register processing using cvs_avg35_inMNI152 as the target. It was also done without errors (in several hours) producing all the expected output files. However, when checking the results of the first step, the spherical registration, the original lh.pial and the resampled lh.resample.pial look almost identical as do the parcellation annotations lh.apac.annot and lh.resample.aparc.annot. Please see a screenshot (the original lh.pial is on the right): [cid:image002.png@01D152A7.B90120D0]
Did the spherical registration perhaps failed (/is buggy) or maybe this is how it is supposed to look like? Please explain! And if it did fail what could I do to fix it? Note that I am using freesurfer-Linux_centos6_x86_64-stable-pub-v5.3.0 from 14th of May, 2013. The final CVS-normalized T1 MR does look like the template.
Thank you,
Zsolt
freesurfer@nmr.mgh.harvard.edu
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dgw -
Douglas N Greve -
Jasmin Alves -
Zsolt Cselényi