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 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] *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 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> wrote:

Just so its clear.. You have installed FreeSurfer on 15 Linux

machines

...

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 simply typing

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>>
 > /
 > /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
 >
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...

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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
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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=/

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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 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.