Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the
suffix i686 instead of i386, so try
sudo yum remove libXp.i686
By removing the 32-bit version you essential ensure only the 64-bit version is
available when the application tries to load libXp. Hope that works. My machine
only has the 64-bit version installed. Although technically, it should not
matter if you have both installed on the system as it should automatically pick
the correction version.
If it doesn't work, you could try to run
find / -type f -iname "libXp.so*" -print
to check if the libXp libraries might be installed somewhere else. It may take some
time to scan the entire system and any mounted volumes. You can use the `file
<file>` command to check if the library is 32 or 64-bit, and remove any 32-bit
or even 64-bit version outside /usr/lib64 (BEWARE: removing libraries is at risk of
breaking functioning of other application that depend on that particular library. If
necessary, you can always run `sudo yum install libXp.i686` to install the 32-bit
version again)
On Jun 29, 2015, at 08:10 AM, Thục Trinh <thuctrinh...@gmail.com> wrote:
Hi,
"yum remove libXp.i386" command returns with
No Packages marked for removal
This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni'
/usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, stripped
2015-06-26 16:19 GMT+07:00 Jalmar Teeuw <jal...@me.com>:
Have you tried removing the 32-bit version of the libraries?
I believe it is
yum remove libXp.i386
What is the output of
file $FREESURFER_HOME/bin/3dvolreg.afni
Maybe you could try locate all the libXp.so on your system and see if there is
a local 32-bit copy
find / -type f -iname "libXp.so*"
On 25 Jun 2015, at 09:45, Thục Trinh <thuctrinh...@gmail.com> wrote:
the lib files are now in /usr/lib64, the ERROR still the same after I set a new
path for shared lib with this command in .bashrc file
export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
the Error still the same.
3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32
output of uname -a on my system is:
Linux localhost.localdomain 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
2015-06-25 14:15 GMT+07:00 Jalmar Teeuw <jal...@me.com>:
Is still gives you the same error? I'm not certain about libXpm; I recall
having to install certain libraries on a slimmed down version of Centos 6.5,
libXp and libXpm were amongst those libraries.
For me, the lib files are stored in /usr/lib64
Try
find /usr/lib64 -type f -iname "libXp*" -print
This will search for the files.
What is the output
uname -a
On your system?
On 25 Jun 2015, at 09:01, Thục Trinh <thuctrinh...@gmail.com> wrote:
Hi,
After complete install the suitable version of shared library as you suggested,
I cannot find any file name libXpm.x86_64 to set the new path for shared
library.
Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64
2015-06-24 16:03 GMT+07:00 Jalmar Teeuw <jal...@me.com>:
That sounds more like you have only the 32-bit version of the libXp installed
when 64-bit is required. Are you using the 64-bit version of Freesurfer 5.3.0
for CentOS 6 that is available on the downloads page?
Have you tried
sudo yum install libXp.x86_64
on the terminal? This should install the 64-bit libraries alongside the 32-bit
libraries of libXp.
If I recall correctly, you might also need the libXpm libraries, use
sudo yum install libXpm.x86_64
On 24 Jun 2015, at 04:49, Thục Trinh <thuctrinh...@gmail.com> wrote:
I did that, and run the command 3dvolreg.afni on Terminal to check.
The Error still remain: 3dvolreg.afni: error while loading shared libraries:
libXp.so.6: wrong ELF class: ELFCLASS32
2015-06-23 10:39 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>:
From reading the email thread history, it appears you may have downloaded the
apple OS X version of 3rvolreg.afni and overwrote the original, which is the
cause of the error. Please extract the original version of that binary from the
original tarball. If you no longer have it you can download it from this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
On Jun 22, 2015, at 11:29 PM, Thục Trinh <thuctrinh...@gmail.com> wrote:
hello,
I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0.
I think that makes the confliction.
2015-06-23 8:26 GMT+07:00 Thục Trinh <thuctrinh...@gmail.com>:
Hello Douglas and ZK,
I set the path for shared library in my .basrch file, but it still does not
work and comes up with this Error:
3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF
class: ELFCLASS32
ERROR: 3dvolreg.afni
Invalid null command.
Trinh
2015-06-23 3:03 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>:
Trinh,
Attempt to determine where libXp.so.6 was installed on your system after
you installed it using yum. For example, on my system libXp.so.6 exists
in directory "/usr/lib64". Once you determine the location where the
library resides, add that directory to your LD_LIBRARY_PATH after you
source freesurfer.
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh
$> export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
$> preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh
-fwhm 5 -per-run
-Zeke
On 06/22/2015 02:40 PM, Douglas Greve wrote:
> I'm not sure what to tell you. Zeke, do you have any ideas?
> Alternatively, you can just install afni on your machine. Once you
> verify that the installation works, copy 3dvolreg from the installation.
>
> On 6/21/15 3:55 PM, Thục Trinh wrote:
>> Hello Douglas,
>> I already had *3dvolreg.afni* in */freesurfer/bin/*, but I still
>> download the new one 3dvolreg.afni and replaced it in /freesurfer/bin.
>> But the Error still remain the same.
>> *3dvolreg.afni: error while loading shared libraries: libXp.so.6:
>> cannot open shared object file: No such file or directory*
>> *ERROR: 3dvolreg.afni*
>> *Invalid null command.*
>>
>>
>> 2015-06-19 16:04 GMT+07:00 Douglas Greve <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>:
>>
>>
>> See this thread
>>
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
>>
>>
>>
>>
>> On 6/17/15 5:59 PM, Thục Trinh wrote:
>>> Hi freesurfer experts,
>>> I am practicing on the fsfast tutorial data that were given at
>>> Freesurfer website.
>>> I run the command to do the pre-processing on the sess01 <*noproc*>.
>>> *preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh
>>> -fwhm 5 -per-run*
>>> it was unfinished and failed with the ERROR:
>>> *3dvolreg.afni: error while loading shared libraries: libXp.so.6:
>>> cannot open shared object file: No such file or directory*
>>> *ERROR: 3dvolreg.afni*
>>> *Invalid null command.*
>>> so I run the command to install libXp.so.6 under root permission
>>> *yum install libXp.so.6 *and completely installed.
>>> I found the file *3dvolreg.afni *in the $FREESURFER_HOME/bin
>>> But the ERROR still remained unfixed.
>>>
>>> Please help me with any suggestions to finish the preproc-sesss
>>> Thankyou and have a nice day.
>>> Trinh Tran
>>>
>>>
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>>
>>
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