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 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 / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/

---

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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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
 >
_______________________________________________
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=/

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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
 >
_______________________________________________
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=/

---

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---

Freesurfer mailing list 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 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

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.

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 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>

...

<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.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=/

---

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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/

/webpage: //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/

/webpage: //http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/

---

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Dear Bruce,

Thanks for your email, for some reasons your email went to the spam folder.

Yes, all PC are running Ubuntu.

The ram is: 7.6 GiB

Processor: Intel® Core™ i7-3770 CPU @ 3.40GHz × 8

The graphic card: Intel® Ivybridge Desktop

*-display description: VGA compatible controller product: Xeon E3-1200 v2/3rd Gen Core processor Graphics Controller vendor: Intel Corporation physical id: 2 bus info: pci@0000:00:02.0 version: 09 width: 64 bits clock: 33MHz capabilities: msi pm vga_controller bus_master cap_list rom configuration: driver=i915 latency=0 resources: irq:44 memory:f7800000-f7bfffff memory:e0000000-efffffff ioport:f000(size=64)

Thanks, Ali

On Tue, Aug 5, 2014 at 11:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Ali

they are all running ubuntu? How much ram is in them? Wha version of FreeSurfer and what version of ubuntu? What graphics cards do you have?

cheers Bruce

On Tue, 5 Aug 2014, 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 webpage: 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.