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 
Date: Sunday, March 11, 2018 at 6:30 AM
To: "Hoopes, Andrew" 
Cc: FS Help 
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 
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*
> ___
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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.
>



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

[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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[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] 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 

> 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  > >
> >
> > 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
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 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
> 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
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> but does not contain patient information, please contact the sender and
> properly
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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  >
>
> 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
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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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 

> 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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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

[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"  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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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"  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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>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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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

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

[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
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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

[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  
> > -…... ” 
> > 
> > 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/SetUpFreeSurfe

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  
> -…... ” 
> 
> 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”
> > > > &

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  
-…... ” 

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  
> > > > 
> > > > 
> > > > 
> > > > -…... ” 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

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  
> > > 
> > > 
> > > 
> > > -…... ” 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

[Liukarl]

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
> > 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  
> > 
> >  
> > 
> > -…... ” 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


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 

> try the command:
>
> sudo apt-get install tcl
>
> -- PPJ
>
> Please: cc the freesurfer list when answering
>
> 2011/2/22 Carolina Valencia 
>
> 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 
>>
>>> run this command
>>>
>>> sudo rm -rf $FREESURFER_HOME
>>>
>>>
>>>
>>> 2011/2/21 Carolina Valencia 
>>>
 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 
>
>
>> 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 

> 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
>>
>> “

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  
> 
>  
> 
> -…... ” 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

___
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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.

[Freesurfer] installation problem

[Liukarl]

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  
 
-…... ” 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
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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 

> 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 
>
>> run this command
>>
>> sudo rm -rf $FREESURFER_HOME
>>
>>
>>
>> 2011/2/21 Carolina Valencia 
>>
>>> 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 >> >
>>>
 It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS


 2011/2/21 Carolina Valencia 


> 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 
>>>
 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 
>
>  -…...
> ”
> 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@nm

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 

> 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 
>
>> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS
>>
>>
>> 2011/2/21 Carolina Valencia 
>>
>>
>>> 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 >> >
>>>
>>> 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 
>
>> 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 
>>>
>>>  -…...
>>> ”
>>> 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 Compl

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 

>
> 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 
>
> Please send the result of the command:
>>
>> uname -a
>>
>>
>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia > > 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 
>>>
 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 
>
>  -…...
> ”
> 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 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 information, please contact the

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 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 
>
>> 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 
>>>
>>>  -…...
>>> ”
>>> 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 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 information, please contact the sender and properly
dispose of the e-mail.

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 

> 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 
>>
>>  -…...
>> ”
>> 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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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 

  -¡­...
¡±
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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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
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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 

   -…...
”
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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addressed. If you believe this e-mail was sent to you in error and the e-mail
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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]

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.

[Freesurfer] Freesurfer Installation Problem

[Jaakko Karras]

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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