subject:"\[Freesurfer\] Preproc\-sess failed"

Re: [Freesurfer] Preproc-sess failed

2015-07-01 Thread Thục Trinh

Yay !!! It works finally.
So the problem in the first place is: I got the wrong version of shared
library :)
Thank you so much.


2015-07-01 14:58 GMT+07:00 Jalmar Teeuw :

> Yes, the sudo prefix is optional, but may be required otherwise you get a
> 'not authorized' message (i.e. you need administrative privileges to
> install software and libraries); note 'libXp' is case-sensitive!
>
>   sudo yum install libXp.x86_64
>
> The library will be installed at /usr/lib64/libXp.so.6, a symbolic link to
> /usr/lib64/libXp.so.6.2.0
>
> And try Zeke's advice as well, just to be sure
>
>   export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
>
> You would have to run that command at every new terminal you open, or add
> it to the configuration file of your terminal.
>
> P.S. I removed libXp on my machine, and yes, 3dvolreg.afni complains about
> missing libXp.so.6. After installing it again with the first command, it
> works again.
>
> On Jul 01, 2015, at 06:47 AM, Thục Trinh  wrote:
>
> Is the command line like this:
> yum install libXp.so.6.x86_64
>
> because I did run yum install libXp.so.6 before and it did not work.
>
> 2015-07-01 11:28 GMT+07:00 Z K :
>
>> Yes, and when it is done installing, determine exactly what directory the
>> libXp.so.6 file was installed into. That is the directory you want to add
>> to your LD_LIBRARY_PATH environment variable.
>>
>> -Zeke
>>
>>
>> On Jun 30, 2015, at 11:39 PM, Thục Trinh  wrote:
>>
>> Hi,
>> I did exactly what you said, and the error still remain: *3dvolreg.afni:
>> error while loading shared libraries: libXp.so.6: cannot open shared object
>> file: No such file or directory*
>> I cannot find any folder name libXp.so.6,should I re-download libXp.so.6
>> 64 bits ?
>>
>>
>> 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw :
>>
>>> 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 ` 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  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 :
>>>

 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  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 :

> 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  wrote:
>
> Hi,
> After complete install the suitable version of shared librar

[Freesurfer] Preproc-sess failed

2015-07-01 Thread Jalmar Teeuw


Yes, the sudo prefix is optional, but may be required otherwise you get a 'not 
authorized' message (i.e. you need administrative privileges to install 
software and libraries); note 'libXp' is case-sensitive!

  sudo yum install libXp.x86_64

The library will be installed at /usr/lib64/libXp.so.6, a symbolic link to 
/usr/lib64/libXp.so.6.2.0

And try Zeke's advice as well, just to be sure

  export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH

You would have to run that command at every new terminal you open, or add it to 
the configuration file of your terminal.

P.S. I removed libXp on my machine, and yes, 3dvolreg.afni complains about 
missing libXp.so.6. After installing it again with the first command, it works 
again.

On Jul 01, 2015, at 06:47 AM, Thục Trinh  wrote:

Is the command line like this:
yum install libXp.so.6.x86_64

because I did run yum install libXp.so.6 before and it did not work.

2015-07-01 11:28 GMT+07:00 Z K :
Yes, and when it is done installing, determine exactly what directory the 
libXp.so.6 file was installed into. That is the directory you want to add to 
your LD_LIBRARY_PATH environment variable. 

-Zeke


On Jun 30, 2015, at 11:39 PM, Thục Trinh  wrote:

Hi, 
I did exactly what you said, and the error still remain: 3dvolreg.afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory

I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 
bits ?


2015-06-29 18:15 GMT+07:00 Jalmar Teeuw :
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 
` 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  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 :

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  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 :
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  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 :
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 instal

Re: [Freesurfer] Preproc-sess failed

2015-06-30 Thread Thục Trinh

Is the command line like this:
yum install libXp.so.6.x86_64

because I did run yum install libXp.so.6 before and it did not work.

2015-07-01 11:28 GMT+07:00 Z K :

> Yes, and when it is done installing, determine exactly what directory the
> libXp.so.6 file was installed into. That is the directory you want to add
> to your LD_LIBRARY_PATH environment variable.
>
> -Zeke
>
>
> On Jun 30, 2015, at 11:39 PM, Thục Trinh  wrote:
>
> Hi,
> I did exactly what you said, and the error still remain: *3dvolreg.afni:
> error while loading shared libraries: libXp.so.6: cannot open shared object
> file: No such file or directory*
> I cannot find any folder name libXp.so.6,should I re-download libXp.so.6
> 64 bits ?
>
>
> 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw :
>
>> 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 ` 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  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 :
>>
>>>
>>> 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 $FREESURFER_HOME/bin/3dvolreg.afni
>>>
>>> Maybe you could try locate all the libXp.so on your system and see if
>>> there is a local 32-bit copy
>>>
>>>   find / -type f -iname "libXp.so*"
>>>
>>>
>>> On 25 Jun 2015, at 09:45, Thục Trinh  wrote:
>>>
>>> the lib files are now in /usr/lib64, the ERROR still the same after I
>>> set a new path for shared lib with this command in .bashrc file
>>> *export LD_LIBRARY_PATH=/usr/lib64:$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 :
>>>
 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  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 :

> 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  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

Re: [Freesurfer] Preproc-sess failed

2015-06-30 Thread Z K

Yes, and when it is done installing, determine exactly what directory the 
libXp.so.6 file was installed into. That is the directory you want to add to 
your LD_LIBRARY_PATH environment variable. 

-Zeke


> On Jun 30, 2015, at 11:39 PM, Thục Trinh  wrote:
> 
> Hi, 
> I did exactly what you said, and the error still remain: 3dvolreg.afni: error 
> while loading shared libraries: libXp.so.6: cannot open shared object file: 
> No such file or directory
> I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 
> bits ?
> 
> 
> 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw :
>> 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 ` 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  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 :
 
 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  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 :
>> 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  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 :
 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  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 c

Re: [Freesurfer] Preproc-sess failed

2015-06-30 Thread Thục Trinh

Hi,
I did exactly what you said, and the error still remain: *3dvolreg.afni:
error while loading shared libraries: libXp.so.6: cannot open shared object
file: No such file or directory*
I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64
bits ?


2015-06-29 18:15 GMT+07:00 Jalmar Teeuw :

> 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 ` 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  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 :
>
>>
>> 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 $FREESURFER_HOME/bin/3dvolreg.afni
>>
>> Maybe you could try locate all the libXp.so on your system and see if
>> there is a local 32-bit copy
>>
>>   find / -type f -iname "libXp.so*"
>>
>>
>> On 25 Jun 2015, at 09:45, Thục Trinh  wrote:
>>
>> the lib files are now in /usr/lib64, the ERROR still the same after I set
>> a new path for shared lib with this command in .bashrc file
>> *export LD_LIBRARY_PATH=/usr/lib64:$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 :
>>
>>> 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  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 :
>>>
 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  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 :
 > 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 
 wrote:
 >
 >> hello,
 >> I am using CentOS release 6.4 ( final)

Re: [Freesurfer] Preproc-sess failed

2015-06-29 Thread Jalmar Teeuw


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 
` 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  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 :

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  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 :
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  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 :
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  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 :
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  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 :
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 :
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/SetUp

Re: [Freesurfer] Preproc-sess failed

2015-06-28 Thread Thục Trinh

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 :

> 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 $FREESURFER_HOME/bin/3dvolreg.afni
>
> Maybe you could try locate all the libXp.so on your system and see if
> there is a local 32-bit copy
>
>   find / -type f -iname "libXp.so*"
>
>
> On 25 Jun 2015, at 09:45, Thục Trinh  wrote:
>
> the lib files are now in /usr/lib64, the ERROR still the same after I set
> a new path for shared lib with this command in .bashrc file
> *export LD_LIBRARY_PATH=/usr/lib64:$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 :
>
>> 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  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 :
>>
>>> 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  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 :
>>> > 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 
>>> 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 :
>>> >> 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 :
>>> >> 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

Re: [Freesurfer] Preproc-sess failed

2015-06-26 Thread Jalmar Teeuw

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  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 :
>> 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  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 :
 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  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 :
 > 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  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 :
 >> 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 :
 >> 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

Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Thục Trinh

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 :

> 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  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 :
>
>> 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  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 :
>> > 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 
>> 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 :
>> >> 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 :
>> >> 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 > >> >> >:
>> >> >>
>> >> >>
>> >> >> 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 pr

Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Jalmar Teeuw

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  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 :
>> 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  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 :
>> > 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  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 :
>> >> 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 :
>> >> 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 > >> >> >:
>> >> >>
>> >> >>
>> >> >> 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 libX

Re: [Freesurfer] Preproc-sess failed

2015-06-25 Thread Thục Trinh

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 :

> 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  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 :
> > 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  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 :
> >> 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 :
> >> 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  >> >> >:
> >> >>
> >> >>
> >> >> 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
> >> >>>
> >> >>>
> >> >>> ___
> >> >>> Freesurfer mailing list
> >> >>> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> >>> https://mail.nmr.mgh.harvard.ed

Re: [Freesurfer] Preproc-sess failed

2015-06-24 Thread Jalmar Teeuw

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  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 :
> 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  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 :
>> 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 :
>> 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 > >> >:
>> >>
>> >>
>> >> 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
>> >>>
>> >>>
>> >>> ___
>> >>> 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

Re: [Freesurfer] Preproc-sess failed

2015-06-23 Thread Thục Trinh

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 :

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

Re: [Freesurfer] Preproc-sess failed

2015-06-22 Thread Z K

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

Re: [Freesurfer] Preproc-sess failed

2015-06-22 Thread Thục Trinh

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 :

> 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 :
>
>> 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 > >> >:
>> >>
>> >>
>> >> 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
>> >>>
>> >>>
>> >>> ___
>> >>> Freesurfer mailing list
>> >>> Freesurfer@nmr.mgh.harvard.edu  > Freesurfer@nmr.mgh.harvard.edu>
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu > Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >> The information in this e-mail is intended only for the person to
>> >> whom it is
>> >> addressed. If you believe this e-mail was sent to you in error and
>> >> the e-mail
>> >> contains patient information, please contact the Partners
>> >> Compliance HelpLine at
>> >> http://www.partners.org/complianceline . If the e-mail was sent to
>> >> you in error
>> >> but does not contain patient information, please contact the
>> >> sender and properly
>> >> dispose of the e-mail.
>> >>
>> >>
>> >>
>> >>
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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but

Re: [Freesurfer] Preproc-sess failed

2015-06-22 Thread Thục Trinh

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 :

> 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  >> >:
> >>
> >>
> >> 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
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to
> >> whom it is
> >> addressed. If you believe this e-mail was sent to you in error and
> >> the e-mail
> >> contains patient information, please contact the Partners
> >> Compliance HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in error
> >> but does not contain patient information, please contact the
> >> sender and properly
> >> dispose of the e-mail.
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Preproc-sess failed

2015-06-22 Thread Z K

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 > >:
>>
>>
>> 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
>>>
>>>
>>> ___
>>> 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.
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Preproc-sess failed

2015-06-22 Thread Douglas Greve

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 >:



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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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
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dispose of the e-mail.




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Re: [Freesurfer] Preproc-sess failed

2015-06-21 Thread Thục Trinh

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 :

>
> 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
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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.
>
>
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Re: [Freesurfer] Preproc-sess failed

2015-06-19 Thread Douglas Greve



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


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[Freesurfer] Preproc-sess failed

2015-06-17 Thread Thục Trinh

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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Re: [Freesurfer] Preproc-sess failed

2015-05-18 Thread Douglas Greve

that means that the version of 3dvolreg.afni does not match your 
operating system. What is your OS and what version of FS are you running?


On 5/18/15 4:11 AM, 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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Preproc-sess failed

2015-05-18 Thread Thục Trinh

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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Re: [Freesurfer] Preproc-sess failed for tutorial data

2007-08-08 Thread Doug Greve


You will need to use the most recent development version

doug

lan lin wrote:

I followed the Fsfasttutorial to learn fsfast. But when I run 
preprocessing (preproc-sess -s mgh-101.1 -fwhm 5), I always get 
following error message
 
/san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1

cat: seq.info : No such file or directory
cat: seq.info : No such file or directory
cat: seq.info : No such file or directory
ERROR: seq.info  file does not appear to be formated 
correctly

   Try running fixseqinfo-sess.
ERROR: mc-sess failed
 
 
thanks

Lan



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] Preproc-sess failed for tutorial data

2007-08-08 Thread lan lin

I followed the Fsfasttutorial to learn fsfast. But when I run preprocessing
(preproc-sess -s mgh-101.1 -fwhm 5), I always get following error message

/san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1
cat: seq.info: No such file or directory
cat: seq.info: No such file or directory
cat: seq.info: No such file or directory
ERROR: seq.info file does not appear to be formated correctly
   Try running fixseqinfo-sess.
ERROR: mc-sess failed


thanks
Lan
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[Freesurfer] Preproc-sess failed during smoothing

2005-01-11 Thread Margaret Duff

Hi,  I was trying to preprocess some functional data using the command
preproc-sess -fwhm 6 -sf sessid -df sesspar.  My subjects study directory
is located at /space/troy/1/users/FREESURFER/SM2C2_fsfast/study.  The
command made it through motion correction, then during smoothing gave me
this error:

ERROR:: Environment variable FSLOUTPUTTYPE is not set!
Please make sure that the appropriate configuration file is sourced by
your shell (e.g. by putting it in .profile).
e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
/tmp/ipfsl_23657
/space/lyon/1/home/inverse/freesurfer_alpha/fsl/bin/ip fmc fmcsm .1 -s
2.54237288135593220338
ERROR: ip failed
ERROR: ipfsl failed
ERROR: spatialsmooth-sess failed

I have never received this error before and am not sure if I should just
set the env. variable or where the .profile is.  What is the recommended
course of action and is there any reason I got this error now, and never
before?  Thanks!  Margaret



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Re: [Freesurfer] Preproc-sess failed

[Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

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Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

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Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

[Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

[Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed for tutorial data

[Freesurfer] Preproc-sess failed for tutorial data

[Freesurfer] Preproc-sess failed during smoothing

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