Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied.
I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer
but did not work.
Any ideas why is this happening although I have done the same thing to other PCs and they are working fine.
Thanks in advance, Ali
Try chmod -R a+X freesurfer/bin
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied.
I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer
but did not work.
Any ideas why is this happening although I have done the same thing to other PCs and they are working fine.
Thanks in advance, Ali
-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do?
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~> tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~>
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Try chmod -R a+X freesurfer/bin
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied.
I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer
but did not work.
Any ideas why is this happening although I have done the same thing to other PCs and they are working fine.
Thanks in advance, Ali
--
*Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do?
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~> tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~>
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote:Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ _______________________________________________ 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 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.-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do?
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~> tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~>
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote:Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ _______________________________________________ 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 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.-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you?
-Zeke
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: > Dear Douglas > > Thanks for your reply. unfortunatey I still get the same error. Here is > the terminal output. Is there anything else I can do? > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/local/fsl > imaging@imaging-ThinkCentre-23:~$ tcsh > imaging-ThinkCentre-23:~> tkmedit > /usr/local/freesurfer/bin/tkmedit: Permission denied. > imaging-ThinkCentre-23:~> > > > On Mon, Oct 27, 2014 at 5:21 AM, Douglas 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: > > > Try chmod -R a+X freesurfer/bin > > > On 10/26/14 1:57 PM, Ali Radaideh wrote: >> Dear FreeSurfer users, >> >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the >> PCs has the latest version of freesurfer 5.3.0 while the others >> have the version 5.0.0. The PC that is installed with the latest >> version freesurfer 5.3.0 does not allow me to run any command and >> everytime I try a command such such as tkmedit i get the following >> error >> /usr/local/freesurfer/bin/tkmedit: permission denied. >> >> I have tried to change the permission settings >> sudo chown -R imaging:imaging freesurfer >> >> but did not work. >> >> Any ideas why is this happening although I have done the same >> thing to other PCs and they are working fine. >> >> Thanks in advance, >> Ali >> >> -- >> /Ali M. Al-Radaideh. PhD >> Assistant Professor >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> >> / >> /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Assistant Professor > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Z K,
Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results.
Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab).
To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine)
All these PCs have Ubuntu 14.04 64bit installed on them.
No, I am not using any vitual machine.
Regarding the root user, I will try it on Sunday as I am away for a couple of days.
Many thanks for your continuous support.
Ali
On Thu, Oct 30, 2014 at 6:34 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you?
-Zeke
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: > Dear Douglas > > Thanks for your reply. unfortunatey I still get the same error. Here is > the terminal output. Is there anything else I can do? > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/local/fsl > imaging@imaging-ThinkCentre-23:~$ tcsh > imaging-ThinkCentre-23:~> tkmedit > /usr/local/freesurfer/bin/tkmedit: Permission denied. > imaging-ThinkCentre-23:~> > > > On Mon, Oct 27, 2014 at 5:21 AM, Douglas 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: > > > Try chmod -R a+X freesurfer/bin > > > On 10/26/14 1:57 PM, Ali Radaideh wrote: >> Dear FreeSurfer users, >> >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the >> PCs has the latest version of freesurfer 5.3.0 while theothers
>> have the version 5.0.0. The PC that is installed with thelatest
>> version freesurfer 5.3.0 does not allow me to run any command and >> everytime I try a command such such as tkmedit i get the following >> error >> /usr/local/freesurfer/bin/tkmedit: permission denied. >> >> I have tried to change the permission settings >> sudo chown -R imaging:imaging freesurfer >> >> but did not work. >> >> Any ideas why is this happening although I have done the same >> thing to other PCs and they are working fine. >> >> Thanks in advance, >> Ali >> >> -- >> /Ali M. Al-Radaideh. PhD >> Assistant Professor >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> >> / >> /webpage:http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 theperson 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 sentto
> you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > > -- > /Ali M. Al-Radaideh. PhD > Assistant Professor > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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
Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight.
-Zeke
Hi Z K,
Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results.
Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab).
To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine)
All these PCs have Ubuntu 14.04 64bit installed on them.
No, I am not using any vitual machine.
Regarding the root user, I will try it on Sunday as I am away for a couple of days.
Many thanks for your continuous support.
Ali
On Thu, Oct 30, 2014 at 6:34 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you?
-Zeke
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: > Dear Douglas > > Thanks for your reply. unfortunatey I still get the same error. Here is > the terminal output. Is there anything else I can do? > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/local/fsl > imaging@imaging-ThinkCentre-23:~$ tcsh > imaging-ThinkCentre-23:~> tkmedit > /usr/local/freesurfer/bin/tkmedit: Permission denied. > imaging-ThinkCentre-23:~> > > > On Mon, Oct 27, 2014 at 5:21 AM, Douglas 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: > > > Try chmod -R a+X freesurfer/bin > > > On 10/26/14 1:57 PM, Ali Radaideh wrote: >> Dear FreeSurfer users, >> >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the >> PCs has the latest version of freesurfer 5.3.0 while theothers
>> have the version 5.0.0. The PC that is installed with thelatest
>> version freesurfer 5.3.0 does not allow me to run any command and >> everytime I try a command such such as tkmedit i get the following >> error >> /usr/local/freesurfer/bin/tkmedit: permission denied. >> >> I have tried to change the permission settings >> sudo chown -R imaging:imaging freesurfer >> >> but did not work. >> >> Any ideas why is this happening although I have done thesame
>> thing to other PCs and they are working fine. >> >> âThanks in advance, >> Aliâ >> >> -- >> /Ali M. Al-Radaideh. PhD >> Assistant Professor >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> >> / >> /webpage:http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 theperson 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 sentto
> you in error > but does not contain patient information, please contactthe
sender > and properly > dispose of the e-mail. > > > > > -- > /Ali M. Al-Radaideh. PhD > Assistant Professor > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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--
*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi
I’ve previously encountered the same error. I’ve also tried to change permission but that didn’t really work out for me. I have fixed it by installing libjpeg62-dev: Maybe the following command could fix your problem too?
sudo apt-get install libjpeg62-dev
Hope this might work for you?
Cheers
Robby
Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent
Robby.DePauw@Ugent.be
On 31 Oct 2014, at 16:35, zkaufman@nmr.mgh.harvard.edu wrote:
Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight.
-Zeke
Hi Z K,
Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results.
Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab).
To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine)
All these PCs have Ubuntu 14.04 64bit installed on them.
No, I am not using any vitual machine.
Regarding the root user, I will try it on Sunday as I am away for a couple of days.
Many thanks for your continuous support.
Ali
On Thu, Oct 30, 2014 at 6:34 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you?
-Zeke
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error.
Here is
the terminal output. Is there anything else I can do?
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~> tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~>
On Mon, Oct 27, 2014 at 5:21 AM, Douglas 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:
Try chmod -R a+X freesurfer/bin
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
of the
PCs has the latest version of freesurfer 5.3.0 while the
others
have the version 5.0.0. The PC that is installed with the
latest
version freesurfer 5.3.0 does not allow me to run any
command and
everytime I try a command such such as tkmedit i get the
following
error /usr/local/freesurfer/bin/tkmedit: permission denied.
I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer
but did not work.
Any ideas why is this happening although I have done the
same
thing to other PCs and they are working fine.
âThanks in advance, Aliâ
-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo
<mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo>>
/ /webpage:
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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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.
-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo>
<mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo>>
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-- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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--
*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo <ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Try this chmod -R a+x freesurfer/bin/*
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: > Dear Douglas > > Thanks for your reply. unfortunatey I still get the same error. Here is > the terminal output. Is there anything else I can do? > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/local/fsl > imaging@imaging-ThinkCentre-23:~$ tcsh > imaging-ThinkCentre-23:~> tkmedit > /usr/local/freesurfer/bin/tkmedit: Permission denied. > imaging-ThinkCentre-23:~> > > > On Mon, Oct 27, 2014 at 5:21 AM, Douglas 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: > > > Try chmod -R a+X freesurfer/bin > > > On 10/26/14 1:57 PM, Ali Radaideh wrote: >> Dear FreeSurfer users, >> >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the >> PCs has the latest version of freesurfer 5.3.0 while the others >> have the version 5.0.0. The PC that is installed with the latest >> version freesurfer 5.3.0 does not allow me to run any command and >> everytime I try a command such such as tkmedit i get the following >> error >> /usr/local/freesurfer/bin/tkmedit: permission denied. >> >> I have tried to change the permission settings >> sudo chown -R imaging:imaging freesurfer >> >> but did not work. >> >> Any ideas why is this happening although I have done the same >> thing to other PCs and they are working fine. >> >> Thanks in advance, >> Ali >> >> -- >> /Ali M. Al-Radaideh. PhD >> Assistant Professor >> Head of Department of Medical Imaging >> Vice Dean of the Faculty of Allied Health Sciences >> The Hashemite University, >> Zarqa, Jordan >> W.phone +962 5 3903333 ext.5422, 5355, 5364 >> Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> >> / >> /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Assistant Professor > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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-- /Ali M. Al-Radaideh. PhD Assistant Professor Head ofDepartment of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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-
Ali Radaideh -
Douglas Greve -
Douglas N Greve
-
Robby De Pauw -
Z K -
zkaufman＠nmr.mgh.harvard.edu