[Freesurfer] error while loading shared libraries:libtiff.so.3

[Lúcia Garrido]

Hello,

I'm using Debian and downloaded
freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz.

Everything worked fine when I tested the installation with tkmedit and tksurfer.
I then ran
recon-all -i C04_SS.nii -autorecon1 -s C04_SS
and it also finished without errors.

But when I ran recon-all -autorecon2 -s C04_SS,
there was an error at the end saying:
mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot
open shared object file: No such file or directory

I've checked the shared libraries and I have libtiff.so.4. Could you let me know
how to get libtiff.so.3 to work and if I should do something else?

Thank you very much.

Lucia

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

[Freesurfer] error while loading shared libraries:libtiff.so.3

[lan lin]

I'm using 64 bit Ubuntu and installed
freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz
Everything worked fine when I tested the installation with tkmedit and
tksurfer.
I then ran recon-all and got error message  while loading shared
libraries:libtiff.so.3.
I have tried
ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

But still got same error message.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

[Daniel Ferreira Padilla]

Dear all,

 

I'm using Ubuntu 10.10 and have the same problem only when working with 4.5
version (I also use 5.1 version without any problem).

 

I have followed previous suggestions making a symbolic link named
libtiff.so.3, but it gives me back the message "denied permission".
 
Also tried to install it with "sudo aptitude install ia32-libs" but it did
not recognize "aptitude" command. So I tried with "sudo apt-get install
ia32-libs" instead and it was ok, but I am still having the same problem.
 
So, what could I do? Can I download libtiff.so.3 from somewhere? How can I
avoid that "denied permission"?
 
Thank you very much for your help.
 
Daniel Ferreira

 

 

#
#@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011
/home/neuroimagen/DANI/subjects/uu0148_36_1/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1 

mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot
open shared object file: No such file or directory
Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC
2011 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011

 

___
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] error while loading shared libraries:libtiff.so.3

[Krish Subramaniam]

Hi Daniel

You get permission denied because you need write permissions for /usr/ 
lib ( wherever libtiff.so.3 is ).

If you think you have the permissions, prefix your "ln" command with a  
"sudo" and it'll ask for your password, and that should work  
successfully.

If you don't have permissions, you need to ask your system  
administrator to do so.

-Krish

On Jun 20, 2011, at 5:44 AM, Daniel Ferreira Padilla wrote:

> Dear all,
>
> I’m using Ubuntu 10.10 and have the same problem only when working  
> with 4.5 version (I also use 5.1 version without any problem).
>
> I have followed previous suggestions making a symbolic link named  
> libtiff.so.3, but it gives me back the message “denied permission”.
>
> Also tried to install it with “sudo aptitude install ia32-libs” but  
> it did not recognize “aptitude” command. So I tried with “sudo apt- 
> get install ia32-libs” instead and it was ok, but I am still having  
> the same problem.
>
> So, what could I do? Can I download libtiff.so.3 from somewhere? How  
> can I avoid that “denied permission”?
>
> Thank you very much for your help.
>
> Daniel Ferreira
>
>
> #
> #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011
> /home/neuroimagen/DANI/subjects/uu0148_36_1/mri
>
>  mris_volmask --label_left_white 2 --label_left_ribbon 3 -- 
> label_right_white 41 --label_right_ribbon 42 --save_ribbon -- 
> save_distance uu0148_36_1
>
> mris_volmask.bin: error while loading shared libraries: libtiff.so. 
> 3: cannot open shared object file: No such file or directory
> Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18  
> 18:42:20 UTC 2011 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011
>
> ___
> 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] error while loading shared libraries:libtiff.so.3

[Daniel Ferreira Padilla]

Thanks Jordi, thanks Krish,

The problem goes on.

I have checked my libtiff files ($ sudo apt-cache search libtiff) and have
got exactly the same as you, Jordi. The problem is that libtiff.so.3 is not
between them.

I also managed to do the symbolic link with sudo ln -sf usr/lib/libtiff.so.4
/usr/lib/libtiff.so.3. So, as I have 6 different lib folders I have created
this libtiff.so.3 link in each one of them, cause I do not know where
recon-all is pointing to.

So, these are my lib folders:
/lib
/lib32
/lib64
/usr//lib
/usr//lib32
/usr/ /lib64 

Only in those three folders inside /usr/ have got the following files:



pngtools - series of tools for PNG (Portable Network Graphics) images
libtiff-doc - TIFF manipulation and conversion documentation
libtiff-tools - TIFF manipulation and conversion tools
libtiff4 - Tag Image File Format (TIFF) library
libtiff4-dev - Tag Image File Format library (TIFF), development files
libtiffxx0c2 - Tag Image File Format (TIFF) library -- C++ interface
libtiff-opengl - TIFF manipulation and conversion tools

So, perhaps recon-all is pointing to libs outside /usr/, where I do not have
these files. Should I paste them on it? And how can I do it by command line?

Please, any other idea?

Thank you very much

Daniel

 

 

 

2011/6/20 Krish Subramaniam < 
kr...@nmr.mgh.harvard.edu>

Hi Daniel

You get permission denied because you need write permissions for /usr/lib (
wherever libtiff.so.3 is ).

If you think you have the permissions, prefix your "ln" command with a
"sudo" and it'll ask for your password, and that should work successfully.

If you don't have permissions, you need to ask your system administrator to
do so.

-Krish



On Jun 20, 2011, at 5:44 AM, Daniel Ferreira Padilla wrote:

Dear all,

I'm using Ubuntu 10.10 and have the same problem only when working with 4.5
version (I also use 5.1 version without any problem).

I have followed previous suggestions making a symbolic link named
libtiff.so.3, but it gives me back the message "denied permission".

Also tried to install it with "sudo aptitude install ia32-libs" but it did
not recognize "aptitude" command. So I tried with "sudo apt-get install
ia32-libs" instead and it was ok, but I am still having the same problem.

So, what could I do? Can I download libtiff.so.3 from somewhere? How can I
avoid that "denied permission"?

Thank you very much for your help.

Daniel Ferreira


#
#@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011
/home/neuroimagen/DANI/subjects/uu0148_36_1/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1

mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot
open shared object file: No such file or directory
Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC
2011 x86_64 GNU/Linux

recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011

___
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] error while loading shared libraries:libtiff.so.3

[Mishkin Derakhshan]

Hi Lucia,
I ran into the problem as well. For me, just making a symbolic link
named libtiff.so.3 which points to libtiff.so.4 seemed to do the
trick. Try this:

ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

(assumes your libs are in /usr/lib/)

hope that helps,
mishkin


On Sat, Mar 29, 2008 at 9:16 AM, Lúcia Garrido <[EMAIL PROTECTED]> wrote:
> Hello,
>
>  I'm using Debian and downloaded
>  freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz.
>
>  Everything worked fine when I tested the installation with tkmedit and 
> tksurfer.
>  I then ran
>  recon-all -i C04_SS.nii -autorecon1 -s C04_SS
>  and it also finished without errors.
>
>  But when I ran recon-all -autorecon2 -s C04_SS,
>  there was an error at the end saying:
>  mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot
>  open shared object file: No such file or directory
>
>  I've checked the shared libraries and I have libtiff.so.4. Could you let me 
> know
>  how to get libtiff.so.3 to work and if I should do something else?
>
>  Thank you very much.
>
>  Lucia
>
>  ___
>  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

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

[Nick Schmansky]

Ian,

Your best bet is to install the libtiff.so.3 rpms.

Nick


On Wed, 2008-08-13 at 12:35 -0700, lan lin wrote:
> I'm using 64 bit Ubuntu and installed  freesurfer-Linux-rh9-stable-
> pub-v4.0.5-full.tar.gz 
> 
> Everything worked fine when I tested the installation with tkmedit and
> tksurfer.
> I then ran recon-all and got error message  while loading shared
> libraries:libtiff.so.3.
> I have tried 
> ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
>  
> But still got same error message.
> ___
> 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

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

[Mark J. Pearrow]

libtiff.so.3 is typically provided by the ia32-libs package in Ubuntu  
and Debian (and presumably any other Debian-derived distros)


So you can install using the following command:

sudo aptitude install ia32-libs

I'm not sure which binary is doing the complaining, I don't see  
anything in $FREESURFER_HOME/bin that is linked against libtiff3 but I  
remember having to install the 32-bit compat library to make stuff work.


HTH,

mjp

On Aug 13, 2008, at 3:35 PM, lan lin wrote:

I'm using 64 bit Ubuntu and installed  freesurfer-Linux-rh9-stable- 
pub-v4.0.5-full.tar.gz


Everything worked fine when I tested the installation with tkmedit  
and tksurfer.
I then ran recon-all and got error message  while loading shared  
libraries:libtiff.so.3.

I have tried
ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

But still got same error message.
___
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

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

[bin.lv]

My system is also 64 bit Ubuntu and met the same problem.
while doing 
   ln -sf usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 
It works ok, so I guess you can try to create soft link instead of hard link~~

bin lv


2008-08-14 



bin.lv 



发件人： lan lin 
发送时间： 2008-08-14  03:37:38 
收件人： freesurfer@nmr.mgh.harvard.edu 
抄送： 
主题： [Freesurfer] error while loading shared libraries:libtiff.so.3 
 
I'm using 64 bit Ubuntu and installed  
freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz 
Everything worked fine when I tested the installation with tkmedit and tksurfer.
I then ran recon-all and got error message  while loading shared 
libraries:libtiff.so.3.
I have tried 
ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3

But still got same error message.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer