Agreed. Long story short, you need to ask your sys admin to install tcsh and link to it from /bin/tcsh if not already there.
-Zeke
On 08/20/2014 11:48 AM, Krieger, Donald N. wrote:
Hi Ali,
Sorry it didn’t work “out of the box.”
It was kind of a long shot.
That interpreter is for an i86 64bit system running linux.
If you are running a Mac or have a 32bit os or … it will be a problem.
If it’s the right one, it needs to be enabled for execution with the following command:
chmod –v 755 /bin/tcsh
This is system administrator stuff which I’m sure others on the list know much better than me.
I’m sure you can grab the correct version of tcsh for your OS from somewhere on the web.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
Universityof Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh *Sent:* Wednesday, August 20, 2014 8:17 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] tkmedit
Dear Don,
Thanks alot for the attachment. I have installed it as recommended and tried the following and I started to get the error message below
imaging@imaging-ThinkCentre-20:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: Permission denied
When using sudo before the above command and entering the password i get the following message:
imaging@imaging-ThinkCentre-20:~$ sudo tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz sudo: tkmedit: command not found
Any idea???
On Tue, Aug 19, 2014 at 4:26 PM, Krieger, Donald N. <kriegerd@upmc.edu mailto:kriegerd@upmc.edu> wrote:
Hi Ali,
You are missing the tcsh interpreter.
It should be located at /bin/tcsh typically.
It usually comes with the operating system but may not have been installed or may be in the wrong place for freesurfer to find it.
I’ve attached a 64 bit i86 version which is from my installation of Fedora Linus.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
*From:*freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh *Sent:* Tuesday, August 19, 2014 8:06 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] tkmedit
Thanks ZK,
I got the following message: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No such file or directory
On Tue, Aug 12, 2014 at 5:29 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Ali,
I have not encountered this issue before. Could you please provide a screencapture or copy/paste of the terminal output when you type:
$> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz
-Zeke
On 08/12/2014 06:48 AM, Ali Radaideh wrote:
Dear Zeke,
Thanks for your email. For some reasons your email went to the spam
folder
The build-stamps.txt file contents:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
freeview does not work
Thanks, Ali
On Tue, Aug 5, 2014 at 11:44 PM, Z K <zkaufman@nmr.mgh.harvard.edu
mailto:zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu
mailto:zkaufman@nmr.mgh.harvard.edu>> wrote:
Just so its clear.. You have installed FreeSurfer on 15 Linuxmachines
running Ubuntu? If so, can you please provide me with the contents of the build-stamps.txt file in the FREESURFER_HOME directory? Also, could you please inform me if freeview works by simplytyping the
freeview command? $> freeview -Zeke On 08/05/2014 04:32 PM, Ali Radaideh wrote: > Dear FreeSurfer experts, > > I have installed FreeSurfer on multiple machines in our image processing > lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. > However, I have tried to test if freesurfer works or not by typing the > following: > > tkmedit bert orig.mgz > > > Unfortunately, I have got the following error message on all PCs > > A segfault has occurred. This is not your fault, > : but is most likely an unrecoverable error and has > : made the program unstable. > > > So what would be the error? > > Many 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>
<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=/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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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
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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/
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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/
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