Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error.
Thanks! Ankita
Hello, I am hoping some freesurfer experts can help - I can't seem to be able to run qdec or freeview as I get an error - "error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory". I did run the command that probably links that library, but no luck.
Any advice or direction?
Thanks! Ankita
On Wed, Jan 27, 2016 at 11:19 PM Ankita Chatterjee achat04@gmail.com wrote:
Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error.
Thanks!
Ankita
HI, Please see the solution for this known error below, as given in this list form Zeke some months ago: Good luck, Markus
2015-09-22 6:05 GMT+02:00 zkaufman@nmr.mgh.harvard.edu:
Hello,
This is a known when running freesurfer on Ubuntu systems. The solution is addressed in the FAQ section on the frresurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
pecifically, the solution is to go into you system's lib directory and create a symlink as follows:
$> cd /usr/lib/x86_64 (or something similar depending upon exact version) $> sudo ln -s libjpeg.so.8 libjpeg.so.62 $> sudo ln -s libtiff.so.4 libtiff.so.3
This should solve it. Best,
-Zeke
2016-01-30 16:44 GMT+01:00 Ankita Chatterjee achat04@gmail.com:
Hello, I am hoping some freesurfer experts can help - I can't seem to be able to run qdec or freeview as I get an error - "error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory". I did run the command that probably links that library, but no luck.
Any advice or direction?
Thanks! Ankita
On Wed, Jan 27, 2016 at 11:19 PM Ankita Chatterjee achat04@gmail.com wrote:
Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error.
Thanks!
Ankita
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Hello Ankita and Markus,
Under Ubuntu 14.04 LTS, there is already a package that provides this shared library
libjpeg.so.62
sudo apt-get install libjpeg62
______________________
dpkg -L libjpeg62 /. /usr /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libjpeg.so.62.0.0 /usr/share /usr/share/doc /usr/share/doc/libjpeg62 /usr/share/doc/libjpeg62/README.6b1 /usr/share/doc/libjpeg62/copyright /usr/share/doc/libjpeg62/README.gz /usr/share/doc/libjpeg62/changelog.Debian.gz /usr/lib/x86_64-linux-gnu/libjpeg.so.62 <- installs the shared library here
The GNU linker (ld) includes this path from the conf file in
/etc/ld.so.conf.d
more x86_64-linux-gnu.conf
# Multiarch support /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu _________________________
The newer and faster jpeg image library
libjpeg-turbo8 _______________________________ libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON) to accelerate baseline JPEG compression and decompression on x86, x86-64, and ARM systems. On such systems, libjpeg-turbo is generally 2-4x as fast as libjpeg, all else being equal. On other types of systems, libjpeg-turbo can still outperform libjpeg by a significant amount, by virtue of its highly-optimized Huffman coding routines. In many cases, the performance of libjpeg-turbo rivals that of proprietary high-speed JPEG codecs. ________________________________
can also be installed at the same time on a Ubuntu 14.04 LTS system. It will not conflict with the other shared library (it uses a larger version number.)
sudo apt-get install libjpeg-turbo8
______________________________
dpkg -L libjpeg-turbo8 /. /usr /usr/share /usr/share/lintian /usr/share/lintian/overrides /usr/share/lintian/overrides/libjpeg-turbo8 /usr/share/doc /usr/share/doc/libjpeg-turbo8 /usr/share/doc/libjpeg-turbo8/copyright /usr/share/doc/libjpeg-turbo8/changelog.Debian.gz /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 <- installs the shared library here /usr/lib/x86_64-linux-gnu/libjpeg.so.8
______________________________
The "turbo8" library appends the '-turbo8' to the documentation and uses a larger version number for its 'soname'.
Brad Zoltick
____________________________________ From: Markus Gschwind [markus.gschwind@gmail.com] Sent: Saturday, January 30, 2016 5:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error on Linux
HI, Please see the solution for this known error below, as given in this list form Zeke some months ago: Good luck, Markus
2015-09-22 6:05 GMT+02:00 <zkaufman@nmr.mgh.harvard.edumailto:zkaufman@nmr.mgh.harvard.edu>: Hello,
This is a known when running freesurfer on Ubuntu systems. The solution is addressed in the FAQ section on the frresurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
pecifically, the solution is to go into you system's lib directory and create a symlink as follows:
$> cd /usr/lib/x86_64 (or something similar depending upon exact version) $> sudo ln -s libjpeg.so.8 libjpeg.so.62 $> sudo ln -s libtiff.so.4 libtiff.so.3
This should solve it. Best,
-Zeke
2016-01-30 16:44 GMT+01:00 Ankita Chatterjee <achat04@gmail.commailto:achat04@gmail.com>: Hello, I am hoping some freesurfer experts can help - I can't seem to be able to run qdec or freeview as I get an error - "error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory". I did run the command that probably links that library, but no luck.
Any advice or direction?
Thanks! Ankita
On Wed, Jan 27, 2016 at 11:19 PM Ankita Chatterjee <achat04@gmail.commailto:achat04@gmail.com> wrote: Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error.
Thanks!
Ankita
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Ankita Chatterjee -
Markus Gschwind -
Zoltick, Brad (NIH/NIMH) [E]