Re: [Freesurfer] Installation problem

[Hoopes, Andrew]

Hi Neda,

That’s unusual - can you send the output of sourcing the file in a debug shell:

sh -x
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

You’ll probably have to ctrl-c to stop this as well. After running it, can you 
also send the ouput of:

env | sort

thanks,
Andrew


From: Neda Mohammadi <n55moham...@gmail.com>
Date: Sunday, March 11, 2018 at 6:30 AM
To: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Installation problem

Hi Andrew,
Thanks for your reply. It repeat the freesurfer startup message .

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 

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  /Work/Processed_data/freesurfer

MNI_DIR   /usr/local/freesurfer/mni

FSL_DIR   /usr/share/fsl/5.0

Best regards


On Wed, Mar 7, 2018 at 11:56 PM, Hoopes, Andrew 
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Neda,

What’s going on exactly? Is the source command hanging or is it repeatedly 
printing the freesurfer startup message?

best
Andrew



On March 7, 2018 at 3:03:38 AM, Neda Mohammadi 
(n55moham...@gmail.com<mailto:n55moham...@gmail.com>) wrote:
Dear Expert,
I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:
1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 

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  /Work/Processed_data/freesurfer

MNI_DIR   /usr/local/freesurfer/mni

FSL_DIR   /usr/share/fsl/5.0
and I must press Ctrl+C to stop.
What do I do now?

--
Best Regards,
Neda
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--
Best Regards,
Neda
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Re: [Freesurfer] Installation problem

[Neda Mohammadi]

Hi Andrew,

Thanks for your reply. It repeat the freesurfer startup message .

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
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  /Work/Processed_data/freesurfer
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0

Best regards



On Wed, Mar 7, 2018 at 11:56 PM, Hoopes, Andrew 
wrote:

> Hi Neda,
>
> What’s going on exactly? Is the source command hanging or is it repeatedly
> printing the freesurfer startup message?
>
> best
> Andrew
>
>
> On March 7, 2018 at 3:03:38 AM, Neda Mohammadi (n55moham...@gmail.com)
> wrote:
>
> Dear Expert,
>
> I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:
>
> 1. Download and extract into the directory /usr/local
> 2.export FREESURFER_HOME=/usr/local/freesurfer
>
> Its fine, but when I run this step
>
> 3.source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> I receive this message n time
>
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
> 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  /Work/Processed_data/freesurfer
> MNI_DIR   /usr/local/freesurfer/mni
> FSL_DIR   /usr/share/fsl/5.0
>
> and I must press Ctrl+C to stop.
> What do I do now?
>
> --
> *Best Regards,*
> *Neda*
> ___
> 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.
>



-- 
*Best Regards,*
*Neda*
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Re: [Freesurfer] Installation problem

[Hoopes, Andrew]

Hi Neda,

What’s going on exactly? Is the source command hanging or is it repeatedly 
printing the freesurfer startup message?

best
Andrew



On March 7, 2018 at 3:03:38 AM, Neda Mohammadi 
(n55moham...@gmail.com) wrote:

Dear Expert,

I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:

1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
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  /Work/Processed_data/freesurfer
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0

and I must press Ctrl+C to stop.
What do I do now?

--
Best Regards,
Neda
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Installation problem

[Neda Mohammadi]

Dear Expert,

I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:

1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
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  /Work/Processed_data/freesurfer
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0

and I must press Ctrl+C to stop.
What do I do now?

-- 
*Best Regards,*
*Neda*
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Re: [Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Nick,

Thanks very much. I will do as per your suggestion. I am new to Linux and
Ubuntu.

If I am not bothering you too much. I read an article where they compared
the results
from Freesurfer's different versions and about using different OS and
concluded saying that
use the same version and do not upgrade while in the middle of the study.
My collaborators are using
Freesurfer 5.0 and I will be helping them in processing the data (sharing
the data processing and analysis)
so is it ok to use use 5.3.0 or 5.0 is recommended.

Thanks very much again
Venkat


On Wed, Jun 11, 2014 at 12:50 AM, Nick Schmansky, MGH 
ni...@nmr.mgh.harvard.edu wrote:

 Venkat,

 Your system appears to be 32bit distribution, as indicated by 'i686' in
 your output string, but the freesurfer you installed is 64b, indicated
 by 'x86_64' in our filename.  So you will need the 32b dist:

 freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz

 Also, v5.0.0 is pretty old, I'd recommend v5.3.0.

 Nick

 On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote:
  Dear All,
 
 
  I looked into the archives extensively but could not find a solution
  to my problem.
 
 
  I am having Ubuntu  Linux administrator-HP-Pro-3330-MT
  3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686
  i686 i686 GNU/Linux.
 
 
  I tried installing
  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get
  the following error message
 
  mri_convert
  /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file
  not executable.
 
  tkmedit
  /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary
  file not executable.
 
 
  I followed the instruction steps as given in freesurfer wiki. What am
  I doing wrong here?. Is there a installation wiki page for giving
  guidelines for ubuntu freesurfer installation.
 
 
  Thanks, any help will be greatly appreciated as I am trying to install
  freesurfer for the past 3 days without success.
 
 
  Thanks
 
  Venkat
 
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 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
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 properly
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[Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Dear All,

I looked into the archives extensively but could not find a solution to my
problem.

I am having Ubuntu  Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
#46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux.

I tried installing
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the
following error message

mri_convert
/usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
executable.

tkmedit
/usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
not executable.

I followed the instruction steps as given in freesurfer wiki. What am I
doing wrong here?. Is there a installation wiki page for giving guidelines
for ubuntu freesurfer installation.

Thanks, any help will be greatly appreciated as I am trying to install
freesurfer for the past 3 days without success.

Thanks
Venkat
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Re: [Freesurfer] Freesurfer installation problem

[Bruce Fischl]

Hi Venkat

What hardware platform are you running on? And can you run:

ls -l  /usr/local/freesurfer/bin/mri_convert

cheers
Bruce

On Tue, 10 Jun 2014, 
Venkateswaran Rajagopalan wrote:

 Dear All,
 
 I looked into the archives extensively but could not find a solution to my
 problem.
 
 I am having Ubuntu  Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
 #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux.
 
 I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz.
 But I get the following error message
 
 mri_convert
 /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
 executable.
 
 tkmedit
 /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
 not executable.
 
 I followed the instruction steps as given in freesurfer wiki. What am I
 doing wrong here?. Is there a installation wiki page for giving guidelines
 for ubuntu freesurfer installation.
 
 Thanks, any help will be greatly appreciated as I am trying to install
 freesurfer for the past 3 days without success.
 
 Thanks
 Venkat
 

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

Re: [Freesurfer] Freesurfer installation problem

[Nick Schmansky, MGH]

Venkat,

Your system appears to be 32bit distribution, as indicated by 'i686' in
your output string, but the freesurfer you installed is 64b, indicated
by 'x86_64' in our filename.  So you will need the 32b dist:

freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz

Also, v5.0.0 is pretty old, I'd recommend v5.3.0.

Nick

On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote:
 Dear All,
 
 
 I looked into the archives extensively but could not find a solution
 to my problem.
 
 
 I am having Ubuntu  Linux administrator-HP-Pro-3330-MT
 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686
 i686 i686 GNU/Linux.
 
 
 I tried installing
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get
 the following error message 
 
 mri_convert
 /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file
 not executable.
 
 tkmedit
 /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary
 file not executable.
 
 
 I followed the instruction steps as given in freesurfer wiki. What am
 I doing wrong here?. Is there a installation wiki page for giving
 guidelines for ubuntu freesurfer installation.
 
 
 Thanks, any help will be greatly appreciated as I am trying to install
 freesurfer for the past 3 days without success.
 
 
 Thanks
 
 Venkat
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Freesurfer installation problem

[Venkateswaran Rajagopalan]

Hi Bruce,

Thanks very much
What hardware platform are you running on?
Memory: 3.8 GiB
Processor Intel core i3-3220 cpu @3.30 GHz*4
Graphics Intel Ivybridge Desktop x86/MMX/SSE2
OS type 32-bit
Disk 103.1 GB

And can you run: ls -l  /usr/local/freesurfer/bin/mri_convert

I get the following when the run the above -rwxr-xr-x 1 root root 4015444
May 14  2013 /usr/local/freesurfer/bin/mri_convert

Thanks a lot

Venkat



On Tue, Jun 10, 2014 at 6:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Venkat

 What hardware platform are you running on? And can you run:

 ls -l  /usr/local/freesurfer/bin/mri_convert

 cheers
 Bruce

 On Tue, 10 Jun 2014,
 Venkateswaran Rajagopalan wrote:

  Dear All,
 
  I looked into the archives extensively but could not find a solution to
 my
  problem.
 
  I am having Ubuntu  Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic
  #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux.
 
  I tried installing
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz.
  But I get the following error message
 
  mri_convert
  /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not
  executable.
 
  tkmedit
  /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file
  not executable.
 
  I followed the instruction steps as given in freesurfer wiki. What am I
  doing wrong here?. Is there a installation wiki page for giving
 guidelines
  for ubuntu freesurfer installation.
 
  Thanks, any help will be greatly appreciated as I am trying to install
  freesurfer for the past 3 days without success.
 
  Thanks
  Venkat
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
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 HelpLine at
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 properly
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Re: [Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear all,

For the error

 freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
 open shared object file: No such file or directory


sudo apt-get install libjpeg62

did the trick. Freeview is running fine

For the error
*libGL error: failed to load driver: swrast*
*libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

Any ideas?

Thank you in advance!
Markus

2014/1/27 Markus Gschwind markus.gschw...@gmail.com

 Dear experts!

 I installed freesurfer on a machine running Ubuntu 12.04.

 I have got some error messages when testing:

 ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.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
 *freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
 open shared object file: No such file or directory*


 ~$ tkmedit bert orig.mgz
 *libGL error: failed to load driver: swrast*
 *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

 and the same error also for tkurfer.

 Thank you for your help!

 Kind regards,
 Markus


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Re: [Freesurfer] Installation problem on ubuntu 12.04.

[Z K]

Markus,

I have never seen those errors before. But a little googling suggested 
perhaps running the program as follows:

~$ LIBGL_DEBUG=verbose ./tkmedit bert orig.mgz

Im a little at a lose at what else to try because we have freesurfer 
installed on pretty much stock Ubuntu platforms and it runs as expected.
Could you also try typing glxgears and tell me if a 3D window popups 
up displaying turning gears, or perhaps an error message is displayed?

-Zeke

On 01/28/2014 03:40 AM, Markus Gschwind wrote:
 Dear all,

 For the error

 freeview.bin: error while loading shared libraries: libjpeg.so.62:
 cannot open shared object file: No such file or directory


 sudo apt-get install libjpeg62

 did the trick. Freeview is running fine

 For the error
 *libGL error: failed to load driver: swrast*
 *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
 *
 *
 Any ideas?

 Thank you in advance!
 Markus

 2014/1/27 Markus Gschwind markus.gschw...@gmail.com
 mailto:markus.gschw...@gmail.com

 Dear experts!

 I installed freesurfer on a machine running Ubuntu 12.04.

 I have got some error messages when testing:

 ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.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
 *freeview.bin: error while loading shared libraries: libjpeg.so.62:
 cannot open shared object file: No such file or directory*


 ~$ tkmedit bert orig.mgz
 *libGL error: failed to load driver: swrast*
 *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

 and the same error also for tkurfer.

 Thank you for your help!

 Kind regards,
 Markus




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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear Zeke,

Thanks for stepping in!

$ LIBGL_DEBUG=verbose tkmedit bert orig.mgz
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
libGL error: failed to load driver: swrast
Reading /usr/local/freesurfer/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/tktools/tkUtils.tcl

tkmedit seems fine though.


~$ glxgears
libGL error: failed to load driver: swrast
libGL error: Try again with LIBGL_DEBUG=verbose for more details.
21147 frames in 5.1 seconds = 4139.989 FPS
5715 frames in 5.0 seconds = 1135.272 FPS
5716 frames in 5.2 seconds = 1108.204 FPS
5715 frames in 5.1 seconds = 1110.123 FPS
5716 frames in 5.2 seconds = 1104.290 FPS
5455 frames in 5.2 seconds = 1058.021 FPS
etc.

I see three 3D gears (blue, red and green) which kind of wiggle...

I mean, is this error really a problem or could I possible live with it?

Thank you!

Makrus

2014/1/28 Z K zkauf...@nmr.mgh.harvard.edu

 Markus,

 I have never seen those errors before. But a little googling suggested
 perhaps running the program as follows:

 ~$ LIBGL_DEBUG=verbose ./tkmedit bert orig.mgz

 Im a little at a lose at what else to try because we have freesurfer
 installed on pretty much stock Ubuntu platforms and it runs as expected.
 Could you also try typing glxgears and tell me if a 3D window popups
 up displaying turning gears, or perhaps an error message is displayed?

 -Zeke

 On 01/28/2014 03:40 AM, Markus Gschwind wrote:
  Dear all,
 
  For the error
 
  freeview.bin: error while loading shared libraries: libjpeg.so.62:
  cannot open shared object file: No such file or directory
 
 
  sudo apt-get install libjpeg62
 
  did the trick. Freeview is running fine
 
  For the error
  *libGL error: failed to load driver: swrast*
  *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
  *
  *
  Any ideas?
 
  Thank you in advance!
  Markus
 
  2014/1/27 Markus Gschwind markus.gschw...@gmail.com
  mailto:markus.gschw...@gmail.com
 
  Dear experts!
 
  I installed freesurfer on a machine running Ubuntu 12.04.
 
  I have got some error messages when testing:
 
  ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.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
  *freeview.bin: error while loading shared libraries: libjpeg.so.62:
  cannot open shared object file: No such file or directory*
 
 
  ~$ tkmedit bert orig.mgz
  *libGL error: failed to load driver: swrast*
  *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
 
  and the same error also for tkurfer.
 
  Thank you for your help!
 
  Kind regards,
  Markus
 
 
 
 
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 is
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 e-mail
 contains patient information, please contact the Partners Compliance
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dispose of the e-mail.

[Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear experts!

I installed freesurfer on a machine running Ubuntu 12.04.

I have got some error messages when testing:

~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.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
*freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
open shared object file: No such file or directory*


~$ tkmedit bert orig.mgz
*libGL error: failed to load driver: swrast*
*libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

and the same error also for tkurfer.

Thank you for your help!

Kind regards,
Markus
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Re: [Freesurfer] installation problem

[Z K]

Hello Xue,

Via what method are you remotely accessing the Linux cluster? (VNC, 
cygwin, etc) I am not sure if it's your X client or the X server, but 
one of them, or maybe both, possibly lack support for OpenGL.

If you aren't already using a VNC system that there I would try that 
option first.

If you are using VNC and not having any luck, than another potential 
solution is try downloading and install Xming from this page: 
http://www.straightrunning.com/XmingNotes. (Try using the version with 
the PuTTY SSH Client).
Xming is a X server for Windows and all OpenGL rendering will be 
performed on your local machine, which could potentially be quite slow, 
but may be adequate for your needs.

Hope this helps.

-Zeke






On 03/20/2013 11:17 PM, Xue Zhang wrote:
 dear freesurfer experts,
   I tried to install freesurfer in a remote linux cluster, when I completed 
 the installation, and began to run the freesurfer gui use my own windows PC, 
 the command line showed erro belowing information :


 [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
 GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
 display: localhost:11.0


 could anyone tell me the reason why my installation failed?  The video card 
 on cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC 
 video card is AMD Radeon HD 7800 Series.




 regards


 Xue Zhang



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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] installation problem

[Xue Zhang]

thanks, Zeke
I use SSH Secure Shell to make the connection, and before I have used 
xmanager(I was told xmanager can do OpenGL rendering on my local machine, the 
protocol I used in xmanager is also ssh), maybe the protocol is incorrect?
does OpenGL have any hardware requirment? I'm wondering whether the poor video 
card on cluster lead to this problem.
 
thanks again
Xue Zhang 





At 2013-03-21 21:57:12,Z K zkauf...@nmr.mgh.harvard.edu wrote:
Hello Xue,

Via what method are you remotely accessing the Linux cluster? (VNC, 
cygwin, etc) I am not sure if it's your X client or the X server, but 
one of them, or maybe both, possibly lack support for OpenGL.

If you aren't already using a VNC system that there I would try that 
option first.

If you are using VNC and not having any luck, than another potential 
solution is try downloading and install Xming from this page: 
http://www.straightrunning.com/XmingNotes. (Try using the version with 
the PuTTY SSH Client).
Xming is a X server for Windows and all OpenGL rendering will be 
performed on your local machine, which could potentially be quite slow, 
but may be adequate for your needs.

Hope this helps.

-Zeke






On 03/20/2013 11:17 PM, Xue Zhang wrote:
 dear freesurfer experts,
   I tried to install freesurfer in a remote linux cluster, when I completed 
 the installation, and began to run the freesurfer gui use my own windows PC, 
 the command line showed erro belowing information :


 [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
 GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
 display: localhost:11.0


 could anyone tell me the reason why my installation failed?  The video card 
 on cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC 
 video card is AMD Radeon HD 7800 Series.




 regards


 Xue Zhang



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] installation problem

[zkauf...@nmr.mgh.harvard.edu]

I believe you are correct, that the poor card is the most likely 
culprit. The Matrox G200 range are not good at anything graphically 
intensive. If you have adequate permission you could try updating the 
drivers. (http://www.matrox.com/graphics/en/support/drivers/latest/)

Also, try running 'glxinfo' on your PC. If you get output that says 
something along the lines of extension GLX missing on display than 
switching to use an X server that supports glx may solve the issue. If 
you get valid output (doesn't complain about missing glx) than the 
card on your cluster is the problem and Im afraid you might be stuck :(

-Zeke

On 03/21/2013 12:27 PM, Xue Zhang wrote:
 thanks, Zeke
 I use SSH Secure Shell to make the connection, and before I have used 
 xmanager(I was told xmanager can do OpenGL rendering on my local machine, the 
 protocol I used in xmanager is also ssh), maybe the protocol is incorrect?
 does OpenGL have any hardware requirment? I'm wondering whether the poor 
 video card on cluster lead to this problem.

 thanks again
 Xue Zhang





 At 2013-03-21 21:57:12,Z K zkauf...@nmr.mgh.harvard.edu wrote:
 Hello Xue,

 Via what method are you remotely accessing the Linux cluster? (VNC,
 cygwin, etc) I am not sure if it's your X client or the X server, but
 one of them, or maybe both, possibly lack support for OpenGL.

 If you aren't already using a VNC system that there I would try that
 option first.

 If you are using VNC and not having any luck, than another potential
 solution is try downloading and install Xming from this page:
 http://www.straightrunning.com/XmingNotes. (Try using the version with
 the PuTTY SSH Client).
 Xming is a X server for Windows and all OpenGL rendering will be
 performed on your local machine, which could potentially be quite slow,
 but may be adequate for your needs.

 Hope this helps.

 -Zeke






 On 03/20/2013 11:17 PM, Xue Zhang wrote:
 dear freesurfer experts,
I tried to install freesurfer in a remote linux cluster, when I 
 completed the installation, and began to run the freesurfer gui use my own 
 windows PC, the command line showed erro belowing information :


 [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
 GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
 display: localhost:11.0


 could anyone tell me the reason why my installation failed?  The video card 
 on cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC 
 video card is AMD Radeon HD 7800 Series.




 regards


 Xue Zhang



 ___
 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


 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.





 来自网易手机号码邮箱了解更多

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[Freesurfer] installation problem

[Xue Zhang]

dear freesurfer experts,
 I tried to install freesurfer in a remote linux cluster, when I completed the 
installation, and began to run the freesurfer gui use my own windows PC, the 
command line showed erro belowing information :


[wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
display: localhost:11.0


could anyone tell me the reason why my installation failed?  The video card on 
cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC video 
card is AMD Radeon HD 7800 Series.




regards


Xue Zhang___
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.

Re: [Freesurfer] installation problem

[Nick Schmansky]

the SetupFreeSurferEnv.csh file needs to be run.  see installation
instructions:

http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration

n.

On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote:
 Hello, Nick
 
 I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all
 respond as Command not found
 
 two questions:
 
 1) How should I initiate freesufter evey time i turn on the computer?
 
 2) The other day when I installed freesurfer,i typed  “tkmedit bert
 orig.mgz”, it reponded “Illegal instruction”. If I typed in
 “recon-all”, it showed 
 “ Required Arguments: 
  -subjid subjid 
 -process directive…... ” 
 
 and the other arguments.
 
 But when i tried the “recon-all” today, it said Command not found.
 
 Another thing is i installed the freesurfer in my Document folder,
 instead of the local folder. Although i am the administrator, Ubuntu
 would not allow me to move any file to the local folder..
 
 Any idea of the problem of freesurfer in my computer?
 
 thanks
 
 Jie
 
 
 
 
 
  From: ni...@nmr.mgh.harvard.edu
  To: remembe...@hotmail.com
  Date: Wed, 23 Feb 2011 18:32:58 -0500
  CC: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] installation problem
  
  does mri_convert work?
  
  glxgears?
  
  tksurfer?
  
  qdec?
  
  freeview?
  
  your installation should work on ubuntu, as it has for other people,
 so
  i'm a bit at a loss.
  
  n.
  
  On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
   Hello, Nick
   
   the output of uname -a is 
   
   Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21
   17:40:48 UTC 2011 i686 GNU/Linux
   
   thanks 
   
   Jie
   
   
   
   
Subject: Re: [Freesurfer] installation problem
From: ni...@nmr.mgh.harvard.edu
To: remembe...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 23 Feb 2011 11:59:16 -0500

what is the output of 

uname -a


On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
 Hello, Freesurfer experts:
 
 
 
 I emailed some installation problems a couple days ago, but
   haven’t
 answered yet. I am new to freesurfer and try to install the
 newest
 version of freesurfer in Ubuntu system. I closely followed the
 instructions, and the only difference is that I installed it
 in my
 Documents, instead of local folder.
 
 
 
 
 
 Below is the output after “source
   $FREESURFER_HOME/SetUpFreeSurfer.sh”
 
 
 
 
 
  freesurfer-Linux-centos4-stable-pub-v5.0.0  
 
 
 
 Setting up environment for FreeSurfer/FS-FAST (and FSL) 
 
 
 
 FREESURFER_HOME /home/jie/Documents/freesurfer/ 
 
 
 
 FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 
 
 
 
 FSF_OUTPUT_FORMAT nii 
 
 
 
 SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 
 
 
 
 MNI_DIR /ho me/jie/Documents/freesurfer//mni 
 
 
 
 Everything seems fine and I also added the .license file to
 the
   br  freesurfer folder. But when I test it by “tkmedit bert
   orig.mgz”, it
 reponds “Illegal instruction”
 
 
 
 If I type in “recon-all”, it will show 
 
 
 
 “ Required Arguments: 
 
 
 
 -subjid subjid 
 
 
 
 -process directive…... ” and the other arguments.
 
 
 
 
 
 How to fix the problem and make Fressurfer run? Any help is
 appreciated. Thanks a lot!
 
 
 
 
 
 PS: my Ubuntu is 32-bit and choose the 32-bit version
 Freesurfer. 
 
 
 
 Jie
 
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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 i nformation, 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.
  
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Re: [Freesurfer] installation problem

[Liukarl]

Do I need to run the SetupFreeSurferEnv.csh  every time before I start the 
Freesurfer? I thought it is only for initial intallation?
 
PS: even after I run the SetupFreeSurferEnv.csh  when i installed Freesurfer 
the other day, it showed 
 
  freesurfer-Linux-centos4-stable-pub-v5.0.0  
 Setting up environment for FreeSurfer/FS-FAST (and FSL) 
 FREESURFER_HOME /home/jie/Documents/freesurfer/ 
 FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 
FSF_OUTPUT_FORMAT nii 
SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 
 MNI_DIR /ho me/jie/Documents/freesurfer//mni 
 
But it did not work for the test tkmedit bert orig.mgz; it reponded“Illegal 
instruction”
 
Any suggestion for the problem?
 
Thanks
 
Jie


 
 From: ni...@nmr.mgh.harvard.edu
 To: remembe...@hotmail.com
 Date: Sat, 26 Feb 2011 18:30:31 -0500
 CC: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] installation problem
 
 the SetupFreeSurferEnv.csh file needs to be run. see installation
 instructions:
 
 http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
 
 n.
 
 On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote:
  Hello, Nick
  
  I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all
  respond as Command not found
  
  two questions:
  
  1) How should I initiate freesufter evey time i turn on the computer?
  
  2) The other day when I installed freesurfer,i typed “tkmedit bert
  orig.mgz”, it reponded “Illegal instruction”. If I typed in
  “recon-all”, it showed 
  “ Required Arguments: 
  -subjid subjid 
  -process directive…... ” 
  
  and the other arguments.
  
  But when i tried the “recon-all” today, it said Command not found.
  
  Another thing is i installed the freesurfer in my Document folder,
  instead of the local folder. Although i am the administrator, Ubuntu
  would not allow me to move any file to the local folder..
  
  Any idea of the problem of freesurfer in my computer?
  
  thanks
  
  Jie
  
  
  
  
  
   From: ni...@nmr.mgh.harvard.edu
   To: remembe...@hotmail.com
   Date: Wed, 23 Feb 2011 18:32:58 -0500
   CC: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] installation problem
   
   does mri_convert work?
   
   glxgears?
   
   tksurfer?
   
   qdec?
   
   freeview?
   
   your installation should work on ubuntu, as it has for other people,
  so
   i'm a bit at a loss.
   
   n.
   
   On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
Hello, Nick

the output of uname -a is 

Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21
17:40:48 UTC 2011 i686 GNU/Linux

thanks 

Jie




 Subject: Re: [Freesurfer] installation problem
 From: ni...@nmr.mgh.harvard.edu
 To: remembe...@hotmail.com
 CC: freesurfer@nmr.mgh.harvard.edu
 Date: Wed, 23 Feb 2011 11:59:16 -0500
 
 what is the output of 
 
 uname -a
 
 
 On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
  Hello, Freesurfer experts:
  
  
  
  I emailed some installation problems a couple days ago, but
haven’t
  answered yet. I am new to freesurfer and try to install the
  newest
  version of freesurfer in Ubuntu system. I closely followed the
  instructions, and the only difference is that I installed it
  in my
  Documents, instead of local folder.
  
  
  
  
  
  Below is the output after “source
$FREESURFER_HOME/SetUpFreeSurfer.sh”
  
  
  
  
  
   freesurfer-Linux-centos4-stable-pub-v5.0.0  
  
  
  
  Setting up environment for FreeSurfer/FS-FAST (and FSL) 
  
  
  
  FREESURFER_HOME /home/jie/Documents/freesurfer/ 
  
  
  
  FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 
  
  
  
  FSF_OUTPUT_FORMAT nii 
  
  
  
  SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 
  
  
  
  MNI_DIR /ho me/jie/Documents/freesurfer//mni 
  
  
  
  Everything seems fine and I also added the .license file to
  the
br  freesurfer folder. But when I test it by “tkmedit bert
orig.mgz”, it
  reponds “Illegal instruction”
  
  
  
  If I type in “recon-all”, it will show 
  
  
  
  “ Required Arguments: 
  
  
  
  -subjid subjid 
  
  
  
  -process directive…... ” and the other arguments.
  
  
  
  
  
  How to fix the problem and make Fressurfer run? Any help is
  appreciated. Thanks a lot!
  
  
  
  
  
  PS: my Ubuntu is 32-bit and choose the 32-bit version
  Freesurfer. 
  
  
  
  Jie
  
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 The information in this e-mail

Re: [Freesurfer] installation problem

[Liukarl]

Hello, Nick

I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all respond as 
Command not found

two questions:

1) How should I initiate freesufter evey time i turn on the computer?

2) The other day when I installed freesurfer,i typed  “tkmedit bert orig.mgz”, 
it reponded “Illegal instruction”. If I typed in “recon-all”, it showed 
“ Required Arguments: 
 -subjid subjid 
-process directive…... ” 

and the other arguments.

But when i tried the “recon-all” today, it said Command not found.

Another thing is i installed the freesurfer in my Document folder, instead of 
the local folder. Although i am the administrator, Ubuntu would not allow me to 
move any file to the local folder..

Any idea of the problem of freesurfer in my computer?

thanks

Jie





 From: ni...@nmr.mgh.harvard.edu
 To: remembe...@hotmail.com
 Date: Wed, 23 Feb 2011 18:32:58 -0500
 CC: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] installation problem
 
 does mri_convert work?
 
 glxgears?
 
 tksurfer?
 
 qdec?
 
 freeview?
 
 your installation should work on ubuntu, as it has for other people, so
 i'm a bit at a loss.
 
 n.
 
 On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
  Hello, Nick
  
  the output of uname -a is 
  
  Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21
  17:40:48 UTC 2011 i686 GNU/Linux
  
  thanks 
  
  Jie
  
  
  
  
   Subject: Re: [Freesurfer] installation problem
   From: ni...@nmr.mgh.harvard.edu
   To: remembe...@hotmail.com
   CC: freesurfer@nmr.mgh.harvard.edu
   Date: Wed, 23 Feb 2011 11:59:16 -0500
   
   what is the output of 
   
   uname -a
   
   
   On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
Hello, Freesurfer experts:



I emailed some installation problems a couple days ago, but
  haven’t
answered yet. I am new to freesurfer and try to install the newest
version of freesurfer in Ubuntu system. I closely followed the
instructions, and the only difference is that I installed it in my
Documents, instead of local folder.





Below is the output after “source
  $FREESURFER_HOME/SetUpFreeSurfer.sh”





 freesurfer-Linux-centos4-stable-pub-v5.0.0  



Setting up environment for FreeSurfer/FS-FAST (and FSL) 



FREESURFER_HOME /home/jie/Documents/freesurfer/ 



FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 



FSF_OUTPUT_FORMAT nii 



SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 



MNI_DIR /home/jie/Documents/freesurfer//mni 



Everything seems fine and I also added the .license file to the
  br  freesurfer folder. But when I test it by “tkmedit bert
  orig.mgz”, it
reponds “Illegal instruction”



If I type in “recon-all”, it will show 



“ Required Arguments: 



-subjid subjid 



-process directive…... ” and the other arguments.





How to fix the problem and make Fressurfer run? Any help is
appreciated. Thanks a lot!





PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. 



Jie

___
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
  ___
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.

Re: [Freesurfer] installation problem

[Nick Schmansky]

what is the output of 

uname -a


On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
 Hello, Freesurfer experts:
 
  
 
 I emailed some installation problems a couple days ago, but haven’t
 answered yet. I am new to freesurfer and try to install the newest
 version of freesurfer in Ubuntu system. I closely followed the
 instructions, and the only difference is that I installed it in my
 Documents, instead of local folder.
 
  
 
  
 
 Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh”
 
  
 
  
 
  freesurfer-Linux-centos4-stable-pub-v5.0.0  
 
  
 
 Setting up environment for FreeSurfer/FS-FAST (and FSL) 
 
  
 
 FREESURFER_HOME /home/jie/Documents/freesurfer/ 
 
  
 
 FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 
 
  
 
 FSF_OUTPUT_FORMAT nii 
 
  
 
 SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 
 
  
 
 MNI_DIR /home/jie/Documents/freesurfer//mni 
 
  
 
 Everything seems fine and I also added the .license file to the
 freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it
 reponds “Illegal instruction”
 
  
 
 If I type in “recon-all”, it will show 
 
  
 
 “ Required Arguments: 
 
  
 
 -subjid subjid 
 
  
 
 -process directive…... ” and the other arguments.
 
  
 
  
 
 How to fix the problem and make Fressurfer run? Any help is
 appreciated. Thanks a lot!
 
  
 
  
 
 PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. 
 
  
 
 Jie
 
 ___
 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


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.

Re: [Freesurfer] installation problem in ubuntu

[Carolina Valencia]

Dear Pedro,

I would like to start with the tutorials but I don't have permission to copy
the data to the subjects directory, how I can change this?

Best regards,

Carolina

2011/2/22 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 try the command:

 sudo apt-get install tcl

 -- PPJ

 Please: cc the freesurfer list when answering

 2011/2/22 Carolina Valencia cvalen...@linkdx.com.co

 Hi Pedro,

 Finally, I could install it with the license file and the environment is
 properly set without warnings.
 But trying to test it, following the instruction on the wiki page I have a
 problem

 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz
 /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio.

 in the .bashrc I copy the right location of the freesurfer folder
 FREESURFER_HOME=/home/cvalencia/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 run this command

 sudo rm -rf $FREESURFER_HOME



 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co

 Thanks Pedro,

 How I uninstall that version to re-install the correct version?
 I look for some answers and try

 rm -rf $FREESURFER_HOME

 It says that I don't have permission,how I can unistall it, if i'm the
 admin user?

 Thanks in advance,

 Carolina

 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior 
 p...@netfilter.com.br

 It seems you are running the 64-bit version of FreeSurfer in a 32-bit
 OS


 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co


 Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae
 #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux

 Thanks,


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior 
 p...@netfilter.com.br

 Please send the result of the command:

 uname -a


 On Mon, Feb 21, 2011 at 10:31, Carolina Valencia 
 cvalen...@linkdx.com.co wrote:

 Hi Bruce,

 I'm experimenting problems with the installation on Ubuntu too.
 There's is warning in the welcome message, it seems that something
 is missing:

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
 FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
 FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
 MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
 FSL_DIR   /usr/share/fsl/4.1


 I try to test it and it shows
 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
 /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de
 ejecutable incorrecto. Binary file not executable.

 Thanks a lot,

 Carolina

 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I
 closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
 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


 The information in this e-mail is intended only for the person to
 whom it is
 addressed. If you believe 

Re: [Freesurfer] installation problem

[Nick Schmansky]

does mri_convert work?

glxgears?

tksurfer?

qdec?

freeview?

your installation should work on ubuntu, as it has for other people, so
i'm a bit at a loss.

n.

On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
 Hello, Nick
 
 the output of uname -a is 
 
 Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21
 17:40:48 UTC 2011 i686 GNU/Linux
 
 thanks 
 
 Jie
 
 
 
 
  Subject: Re: [Freesurfer] installation problem
  From: ni...@nmr.mgh.harvard.edu
  To: remembe...@hotmail.com
  CC: freesurfer@nmr.mgh.harvard.edu
  Date: Wed, 23 Feb 2011 11:59:16 -0500
  
  what is the output of 
  
  uname -a
  
  
  On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
   Hello, Freesurfer experts:
   
   
   
   I emailed some installation problems a couple days ago, but
 haven’t
   answered yet. I am new to freesurfer and try to install the newest
   version of freesurfer in Ubuntu system. I closely followed the
   instructions, and the only difference is that I installed it in my
   Documents, instead of local folder.
   
   
   
   
   
   Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”
   
   
   
   
   
    freesurfer-Linux-centos4-stable-pub-v5.0.0  
   
   
   
   Setting up environment for FreeSurfer/FS-FAST (and FSL) 
   
   
   
   FREESURFER_HOME /home/jie/Documents/freesurfer/ 
   
   
   
   FSFAST_HOME /home/jie/Documents/freesurfer//fsfast 
   
   
   
   FSF_OUTPUT_FORMAT nii 
   
   
   
   SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects 
   
   
   
   MNI_DIR /home/jie/Documents/freesurfer//mni 
   
   
   
   Everything seems fine and I also added the .license file to the
 br  freesurfer folder. But when I test it by “tkmedit bert
 orig.mgz”, it
   reponds “Illegal instruction”
   
   
   
   If I type in “recon-all”, it will show 
   
   
   
   “ Required Arguments: 
   
   
   
   -subjid subjid 
   
   
   
   -process directive…... ” and the other arguments.
   
   
   
   
   
   How to fix the problem and make Fressurfer run? Any help is
   appreciated. Thanks a lot!
   
   
   
   
   
   PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. 
   
   
   
   Jie
   
   ___
   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

Re: [Freesurfer] installation problem in ubuntu

[Pedro Paulo de Magalhães Oliveira Junior]

try the command:

sudo apt-get install tcl

-- PPJ

Please: cc the freesurfer list when answering

2011/2/22 Carolina Valencia cvalen...@linkdx.com.co

 Hi Pedro,

 Finally, I could install it with the license file and the environment is
 properly set without warnings.
 But trying to test it, following the instruction on the wiki page I have a
 problem

 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz
 /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio.

 in the .bashrc I copy the right location of the freesurfer folder
 FREESURFER_HOME=/home/cvalencia/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 run this command

 sudo rm -rf $FREESURFER_HOME



 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co

 Thanks Pedro,

 How I uninstall that version to re-install the correct version?
 I look for some answers and try

 rm -rf $FREESURFER_HOME

 It says that I don't have permission,how I can unistall it, if i'm the
 admin user?

 Thanks in advance,

 Carolina

 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
 

 It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS


 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co


 Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae
 #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux

 Thanks,


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior 
 p...@netfilter.com.br

 Please send the result of the command:

 uname -a


 On Mon, Feb 21, 2011 at 10:31, Carolina Valencia 
 cvalen...@linkdx.com.co wrote:

 Hi Bruce,

 I'm experimenting problems with the installation on Ubuntu too.
 There's is warning in the welcome message, it seems that something is
 missing:

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
 FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
 FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
 MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
 FSL_DIR   /usr/share/fsl/4.1


 I try to test it and it shows
 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
 /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de
 ejecutable incorrecto. Binary file not executable.

 Thanks a lot,

 Carolina

 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I
 closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
 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


 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 

Re: [Freesurfer] installation problem in ubuntu

[Carolina Valencia]

Hi Bruce,

I'm experimenting problems with the installation on Ubuntu too.
There's is warning in the welcome message, it seems that something is
missing:

 freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
FSL_DIR   /usr/share/fsl/4.1


I try to test it and it shows
cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
/home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable
incorrecto. Binary file not executable.

Thanks a lot,

Carolina

2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
 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
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Re: [Freesurfer] installation problem in ubuntu

[Pedro Paulo de Magalhães Oliveira Junior]

Please send the result of the command:

uname -a

On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.cowrote:

 Hi Bruce,

 I'm experimenting problems with the installation on Ubuntu too.
 There's is warning in the welcome message, it seems that something is
 missing:

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
 FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
 FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
 MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
 FSL_DIR   /usr/share/fsl/4.1


 I try to test it and it shows
 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
 /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable
 incorrecto. Binary file not executable.

 Thanks a lot,

 Carolina

 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
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 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.




 --

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 is
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 contains patient information, please contact the Partners Compliance
 HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] installation problem in ubuntu

[Pedro Paulo de Magalhães Oliveira Junior]

It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS


2011/2/21 Carolina Valencia cvalen...@linkdx.com.co


 Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae
 #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux

 Thanks,


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 Please send the result of the command:

 uname -a


 On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co
  wrote:

 Hi Bruce,

 I'm experimenting problems with the installation on Ubuntu too.
 There's is warning in the welcome message, it seems that something is
 missing:

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
 FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
 FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
 MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
 FSL_DIR   /usr/share/fsl/4.1


 I try to test it and it shows
 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
 /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de
 ejecutable incorrecto. Binary file not executable.

 Thanks a lot,

 Carolina

 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
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 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.




 --

 ___
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 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.





___
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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.

Re: [Freesurfer] installation problem in ubuntu

[Pedro Paulo de Magalhães Oliveira Junior]

run this command

sudo rm -rf $FREESURFER_HOME


2011/2/21 Carolina Valencia cvalen...@linkdx.com.co

 Thanks Pedro,

 How I uninstall that version to re-install the correct version?
 I look for some answers and try

 rm -rf $FREESURFER_HOME

 It says that I don't have permission,how I can unistall it, if i'm the
 admin user?

 Thanks in advance,

 Carolina

 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br

 It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS


 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co


 Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae
 #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux

 Thanks,


 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
 

 Please send the result of the command:

 uname -a


 On Mon, Feb 21, 2011 at 10:31, Carolina Valencia 
 cvalen...@linkdx.com.co wrote:

 Hi Bruce,

 I'm experimenting problems with the installation on Ubuntu too.
 There's is warning in the welcome message, it seems that something is
 missing:

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist
 FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer
 FSFAST_HOME   /home/cvalencia/Descargas/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii
 SUBJECTS_DIR  /home/cvalencia/Descargas/freesurfer/subjects
 MNI_DIR   /home/cvalencia/Descargas/freesurfer/mni
 FSL_DIR   /usr/share/fsl/4.1


 I try to test it and it shows
 cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit
 /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de
 ejecutable incorrecto. Binary file not executable.

 Thanks a lot,

 Carolina

 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Jie,

 what hardware are you using? Is it a 64 bit operating system?

 cheers
 Bruce

 On Sat, 19 Feb 2011, Liukarl wrote:










 Hello, Freesurfer experts:



 I am new to freesurfer and try to
 install the newest version of freesurfer in Ubuntu system. I closely
 followed the instructions, and the only difference is that I
 installed it in my Documents, instead of local folder.



 Below is the output after “source
 $FREESURFER_HOME/SetUpFreeSurfer.sh”



 
 freesurfer-Linux-centos4-stable-pub-v5.0.0 

 Setting up environment for
 FreeSurfer/FS-FAST (and FSL)

 FREESURFER_HOME
 /home/jie/Documents/freesurfer/

 FSFAST_HOME
 /home/jie/Documents/freesurfer//fsfast

 FSF_OUTPUT_FORMAT nii

 SUBJECTS_DIR
 /home/jie/Documents/freesurfer//subjects

 MNI_DIR
 /home/jie/Documents/freesurfer//mni




 Everything seems fine and I also added
 the .license file to the freesurfer folder.



 But when I test it by “tkmedit bert
 orig.mgz”, it reponds “Illegal instruction”



 If I type in “recon-all”, it will
 show

 “ Required Arguments:

  -subjid subjid

  -process directive…...
 ”
 and the other arguments.



 How to fix the problem and make
 Fressurfer run? Any help is appreciated. Thanks a lot!



 Jie


 ___
 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.




 --

 ___
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 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
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 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.








 --

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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] installation problem in ubuntu

[Liukarl]

Hello, Freesurfer experts:



I am new to freesurfer and try to
install the newest version of freesurfer in Ubuntu system. I closely
followed the instructions, and the only difference is that I
installed it in my Documents, instead of local folder.



Below is the output after “source
$FREESURFER_HOME/SetUpFreeSurfer.sh”




freesurfer-Linux-centos4-stable-pub-v5.0.0 

Setting up environment for
FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME  
/home/jie/Documents/freesurfer/

FSFAST_HOME  
/home/jie/Documents/freesurfer//fsfast

FSF_OUTPUT_FORMAT nii

SUBJECTS_DIR 
/home/jie/Documents/freesurfer//subjects

MNI_DIR  
/home/jie/Documents/freesurfer//mni




Everything seems fine and I also added
the .license file to the freesurfer folder.



But when I test it by “tkmedit bert
orig.mgz”, it reponds “Illegal instruction”



If I type in “recon-all”, it will
show 

“ Required Arguments:

   -subjid subjid

   -process directive…...
”
and the other arguments.



How to fix the problem and make
Fressurfer run? Any help is appreciated. Thanks a lot!



Jie
  ___
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.

Re: [Freesurfer] installation problem in ubuntu

[Bruce Fischl]

Hi Jie,

what hardware are you using? Is it a 64 bit operating system?

cheers
Bruce
On Sat, 19 Feb 
2011, Liukarl wrote:












Hello, Freesurfer experts:



I am new to freesurfer and try to
install the newest version of freesurfer in Ubuntu system. I closely
followed the instructions, and the only difference is that I
installed it in my Documents, instead of local folder.



Below is the output after ¡°source
$FREESURFER_HOME/SetUpFreeSurfer.sh¡±




freesurfer-Linux-centos4-stable-pub-v5.0.0 

Setting up environment for
FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME
/home/jie/Documents/freesurfer/

FSFAST_HOME
/home/jie/Documents/freesurfer//fsfast

FSF_OUTPUT_FORMAT nii

SUBJECTS_DIR
/home/jie/Documents/freesurfer//subjects

MNI_DIR
/home/jie/Documents/freesurfer//mni




Everything seems fine and I also added
the .license file to the freesurfer folder.



But when I test it by ¡°tkmedit bert
orig.mgz¡±, it reponds ¡°Illegal instruction¡±



If I type in ¡°recon-all¡±, it will
show

¡° Required Arguments:

  -subjid subjid

  -process directive¡­...
¡±
and the other arguments.



How to fix the problem and make
Fressurfer run? Any help is appreciated. Thanks a lot!



Jie
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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.

Re: [Freesurfer] Freesurfer Installation Problem

[Nick Schmansky]

Jaakko,

The message about the missing talairach.xfm file can be ignored (unless
things stop completely and issue an error message).  The code performs a
relative path search to find the file if it doesnt find it in the hard-
coded path (a historical remnant).

About the Tcl problem, which Linux OS variant is being used?  Freesurfer
does include Tcl/Tk/Tix/BLT (in $FREESURFER_HOME/lib/tcltktixblt) and
'tksurfer' is actually a wrapper script which performs the setup to use
those libs, then calls tksurfer.bin.  This is intended to prevent
conflicts with other Tcl/Tk installations.

Maybe you have an existing Tcl/Tk installation that is conflicting and
not handled by our wrapper script.  Before sourcing the freesurfer setup
file (SetupFreeSurferEnv.csh), can you type the following:

  env | grep TCL
  env | grep LD_LIBRARY_PATH
  which tclsh
  which tclsh8.4

This will tell you if you have an existing installation.

Also, are you trying to run tksurfer locally, or over a network
connection, like VNC?

Nick


On Fri, 2007-01-05 at 12:46 -0800, Jaakko Karras wrote:
 I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server
 running Fedora Core 3 (w/ x86_64), but ran into the following error
 upon testing the installation with the command tkmedit bert
 orig.mgz:
 
 $ tkmedit bert orig.mgz
   Talairach
 transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm 
 does not exist ...
 Loading tal xfm
 file 
 /home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm
 
 The setup script ran flawlessly, producing the following output:
 
 $ source SetUpFreeSurfer.csh
  freesurfer-Linux-centos4-stable-pub-v3.0.4 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer
 FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast
 SUBJECTS_DIR/home/fmri/fmrihome/dti/software/freesurfer/subjects
 MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni
 GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl
 FSL_DIR /home/fmri/fmrihome/fsl
 
 I was able to locate the missing talairach.xfm file in the
 appropriate directory.
 
 On another note, I run into the following tcl/tk error when running
 tksurfer:
 
 Tk_Init failed: Can't find a usable tk.tcl in the following
 directories: 
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 
 /home/
 fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 
 ./li
 b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library
 
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: 
 ca
 n't access ::tk::Priv.:::171.65.48.253:0: parent namespace
 doesn't exist
 can't access ::tk::Priv.:::171.65.48.253:0: parent namespace
 doesn't exist
 while executing
 upvar #0 ::tk::Priv.:::171.65.48.253:0 ::tk::Priv
 (uplevel body line 1)
 invoked from within
 uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv
 (procedure tk::ScreenChanged line 9)
 invoked from within
 tk::ScreenChanged [winfo screen .]
 (file
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
 /tk.tcl line 277)
 invoked from within
 source 
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
 .tcl
 (uplevel body line 1)
 invoked from within
 uplevel #0 [list source $file]
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: 
 ca
 n't import command mc: already exists
 can't import command mc: already exists
 while executing
 namespace import ::msgcat::mc
 (in namespace eval ::tk::msgcat script line 21)
 invoked from within
 namespace eval msgcat {
 namespace export mc mcmax
 if {[interp issafe] || [catch {package require msgcat}]} {
 # The msgcat...
 (in namespace eval ::tk script line 3)
 invoked from within
 namespace eval ::tk {
 # Set up the msgcat commands
 namespace eval msgcat {
 namespace export mc mcmax
 if {[interp issafe] || [...
 (file
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
 /tk.tcl line 20)
 invoked from within
 source 
 /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
 .tcl
 (uplevel body line 1)
 invoked from within
 uplevel #0 [list source $file]
 
 
 This probably means that tk wasn't installed properly.
 
 
 I run into the same error when opening the FSL 3.3 GUI, so I assume
 the error from FreeSurfer is related. I understood that the latest
 FreeSurfer is packaged with the required tcl/tk libraries, so this
 shouldn't be an issue. Any thoughts?
 
 Note: I also installed the standard CentOS 4 (non 64 bit)
 distribution, but encountered the same problems.
 
 Thanks,
 Jaakko
 
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