from:"Thục Trinh"

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

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

2015-06-22 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  >> <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
> >>>
> >>>
> >>> ___
> >>> 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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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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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 > >> <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
>> >>>
>> >>>
>> >>> ___
>> >>> 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

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 >> >> <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 Tra

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  >> >> <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 -surf

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,
>> >> >>

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
>>>

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, Thụ

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

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 librar

[Freesurfer] paradigm file

2015-07-21 Thread Thục Trinh

Hello,
I'm working on fMRI analysis on flattening brain by using FSFAST tool. In
our data, subjects play game: Matrix reasoning. How can I set up the
paradigm file if the duration stimulus depends on the Time response of each
subject following each trial.

Thanks !!
Trinh
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Re: [Freesurfer] paradigm file

2015-07-24 Thread Thục Trinh

Hi,

In our experiment, one onset trial will be lasted for 12 seconds, but if
subject can give the answer sooner within 12 seconds, the next offset trial
(baseline) will come up. The response time will be recorded.
So if I have 100 subjects, I have to create 100 paradigm files manually. It
will cost alot of time. Do you have any suggest to solve this problem.

Thanks

2015-07-22 20:36 GMT+07:00 Douglas Greve :

>  Each entry in the paradigm file represents a presentation characterized
> by 4 values:
> 1. Onset time
> 2. Stimulus code (integer 0-N)
> 3. Stimulus duration
> 4. Weight (usually 1)
>
> If each stimulus presentation has a different duration, then that would be
> indicated in #3
>
> doug
>
>
> On 7/22/15 12:23 AM, Thục Trinh wrote:
>
> Hello,
> I'm working on fMRI analysis on flattening brain by using FSFAST tool. In
> our data, subjects play game: Matrix reasoning. How can I set up the
> paradigm file if the duration stimulus depends on the Time response of each
> subject following each trial.
>
>  Thanks !!
> Trinh
>
>
> ___
> 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
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[Freesurfer] White matter Error

2015-10-01 Thread Thục Trinh


 NCP140539_2_recon.rar

Hi Freesurfer Experts,

We are on the process of troubleshooting our subjects's recon and we came
across with this error that we can not determine what kind of problem this
is:
It seems there is no white matter and pial errors on all slices as we check
on three different views (sagital,coronal and axial);however, when we load
rh.inflated.nofix surface on both freeview and tksurfer, there is a big
difference that at the frontal cortex (area near the medial wall), it
appears a handle error and also some hole errors on freeview while it does
not on tksurfer.
Would you explain how it is visualized that makes us so confused to
troubleshoot since we can not find anything wrong on white matter volume to
be fixed?
Here is our data,

Have a nice day,

Trinh
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Re: [Freesurfer] White matter Error

2015-10-05 Thread Thục Trinh

Hi Bruce,

I did check the output recon by using mris_euler_number, all the results of
?h.pial, ?.white and also ?h.inflated returned with: 0 holes. But the
result from lh.inflated.nofix was: 28 holes.
When I load the 3D images of ?h.inflated.nofix in freeview, it appears alot
of holes and also handles errors.
I wonder about the differences between ?h.inflated and ?h.inflated.nofix.
If we want to estimate the quality of recon output, what images we should
use?

Thanks and Have a nice day,

Trinh

2015-10-02 19:33 GMT+07:00 Bruce Fischl :

> Hi Trinh
>
> can you just attach the images? Your link didn't work for me. You can
> check the topology of the surface computationally using mris_euler_number.
> You might also try moving backwards/forwards a few slices to try to
> understand what is going on.
>
> cheers
> Bruce
>
> On Fri, 2 Oct 2015, Thục Trinh wrote:
>
>
>>
>> [icon_10_generic_list.png]  NCP140539_2_recon.rar
>> Hi Freesurfer Experts,
>>
>> We are on the process of troubleshooting our subjects's recon and we came
>> across with this error that we can not determine what kind of problem this
>> is:
>> It seems there is no white matter and pial errors on all slices as we
>> check
>> on three different views (sagital,coronal and axial);however, when we load
>> rh.inflated.nofix surface on both freeview and tksurfer, there is a big
>> difference that at the frontal cortex (area near the medial wall), it
>> appears a handle error and also some hole errors on freeview while it does
>> not on tksurfer.
>> Would you explain how it is visualized that makes us so confused to
>> troubleshoot since we can not find anything wrong on white matter volume
>> to
>> be fixed?
>> Here is our data,
>>
>> Have a nice day,
>>
>> Trinh
>>
>>
>>
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Re: [Freesurfer] tilted head

2015-10-08 Thread Thục Trinh

They are fine.
Thank you.

2015-10-08 10:06 GMT+07:00 Bruce Fischl :

> I think it should be fine. Do the segmentations and surfaces look accurate?
>
> On Oct 7, 2015, at 10:54 PM, Thục Trinh  wrote:
>
> Hi Freesurfer Experts,
>
> We are on the process of troubleshooting on all of our subjects and come
> across with the problem that we have not faced before.  Here it is:
>
> We have several subjects that their heads were not in a perfectly straight
> line captured by using MRI.  Does that affect to the segmentation of a
> recon, and more importantly somehow carry out some statistical values for
> further analysis (volume, cortical thickness)?
>
> As you can see, Axial view shows the head being tilted to the right.
> Sagital_lh and Sagital_rh images show how the white matter and gray matter
> segmentation are
> being bounded on the same slice 130 but in different hemisphere.
>
> Do we need to do something about it? If yes, how are we going to fix it?
>
> We are greatly appreciated to your patience and hopefully to get your
> response as soon as possible.
>
> Trinh
>
>
> 
>
> 
>
> 
>
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Re: [Freesurfer] White matter Error

2015-10-09 Thread Thục Trinh

Hi Bruce,

I am still confusing about my subjects'recon that I still doubt my skill on
detecting the topological error. Therefore, I practice on the FStutorial
data and run the mris_euler_number on the "topo_defect_before" to see what
happens. The result returns me with 0 holes for all ?h.pial, ?h.white and
?h.inflated.

Can you help me with this problem.

Thank,
Trinh

2015-10-05 23:09 GMT+07:00 Bruce Fischl :

> Hi Trinh
>
> the inflated.nofix files are the ones before the topology fixer so they
> will always have defects in them
>
> cheers
> Bruce
>
> On Mon, 5 Oct 2015, Thục Trinh wrote:
>
> Hi Bruce,
>> I did check the output recon by using mris_euler_number, all the results
>> of
>> ?h.pial, ?.white and also ?h.inflated returned with: 0 holes. But the
>> result
>> from lh.inflated.nofix was: 28 holes.
>> When I load the 3D images of ?h.inflated.nofix in freeview, it appears
>> alot
>> of holes and also handles errors.
>> I wonder about the differences between ?h.inflated and ?h.inflated.nofix.
>> If
>> we want to estimate the quality of recon output, what images we should
>> use?
>>
>> Thanks and Have a nice day,
>>
>> Trinh
>>
>> 2015-10-02 19:33 GMT+07:00 Bruce Fischl :
>>   Hi Trinh
>>
>>   can you just attach the images? Your link didn't work for me.
>>   You can check the topology of the surface computationally using
>>   mris_euler_number. You might also try moving backwards/forwards
>>   a few slices to try to understand what is going on.
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 2 Oct 2015, Thục Trinh wrote:
>>
>>
>>
>> [icon_10_generic_list.png]  NCP140539_2_recon.rar
>> Hi Freesurfer Experts,
>>
>> We are on the process of troubleshooting our
>> subjects's recon and we came
>> across with this error that we can not determine
>> what kind of problem this
>> is:
>> It seems there is no white matter and pial errors on
>> all slices as we check
>> on three different views (sagital,coronal and
>> axial);however, when we load
>> rh.inflated.nofix surface on both freeview and
>> tksurfer, there is a big
>> difference that at the frontal cortex (area near the
>> medial wall), it
>> appears a handle error and also some hole errors on
>> freeview while it does
>> not on tksurfer.
>> Would you explain how it is visualized that makes us
>> so confused to
>> troubleshoot since we can not find anything wrong on
>> white matter volume to
>> be fixed?
>> Here is our data,
>>
>> Have a nice day,
>>
>> Trinh
>>
>>
>>
>>   ___
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>>   contains patient information, please contact the Partners
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>>   dispose of the e-mail.
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>>
>>
>>
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[Freesurfer] wrong segmentation

2015-10-29 Thread Thục Trinh

Hi Freesurfer experts,

I ran recon-all for our subjects and there is a problem with the wrong
segmentation between the white/gray matter. this error appears in couples
continued slices. Picture are attached.
Do you have any suggestion to fix this error.

Thank you,
Trinh
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Re: [Freesurfer] wrong segmentation

2015-11-02 Thread Thục Trinh

I used freesurfer v5.3. We have about 5 subjects that had this kind of
error. We tried to fix on the wm and the result seemed good but we have no
clue to deal with the aseg. Here is the link to my subject directory (no
fix).
http://www.mediafire.com/download/xm2igrdo33mdgmm/NCP140575_1_recon.rar

Thank you and Have a nice day!

Trinh

2015-10-30 23:27 GMT+07:00 Bruce Fischl :

> what version are you using? I think this won't happen in V6,but if you
> upload the subject dir I can check for you. To fix it check and correct the
> wm.mgz and the aseg.mgz in that region
>
> cheers
> Bruce
>
> On Thu, 29 Oct 2015, Thục Trinh wrote:
>
> Hi Freesurfer experts,
>> I ran recon-all for our subjects and there is a problem with the wrong
>> segmentation between the white/gray matter. this error appears in couples
>> continued slices. Picture are attached.
>> Do you have any suggestion to fix this error.
>>
>> Thank you,
>> Trinh
>>
>>
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[Freesurfer] FS v.6.0

2015-11-25 Thread Thục Trinh

Hello Freesurfer experts,

I used recon-all command for all my subject by FS v.5.3. But now I decide
to upgrade to FS v.6 to eliminate some segmentation errors. The pial errors
still appear on the new output of FS v.6 Can I replace the braimask.mgz of
FS v.6 by the brainmask.mgz of FS v.5.3 (that been already fixed) to fixed
all the pial errors,

Have a nice day,
Trinh
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[Freesurfer] missing 3volreg.afni

2015-12-19 Thread Thục Trinh

Hi FS experts,

I'm working on my fMRI data using FSFAST v.6 tool. But the first step of
Preproc-sess was failed with an error :" *ERROR: cannot find AFNI command
3dvolreg.afni ". *
I found a thread that had the same error with mine (in FS v.5.3) :
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html

But the link to download 3dvolreg.afni doesn't work. Is this the same
3dvolreg.afni for v.5.3 and v.6?

Thanks,
Trinh
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Re: [Freesurfer] missing 3volreg.afni

2015-12-22 Thread Thục Trinh

Hi Douglas,
It still does not work.

2015-12-21 23:29 GMT+07:00 Douglas N Greve :

> that link works for me. Can you try again?
>
> On 12/20/2015 02:17 AM, Thục Trinh wrote:
> > Hi FS experts,
> >
> > I'm working on my fMRI data using FSFAST v.6 tool. But the first step
> > of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI
> > command 3dvolreg.afni ". *
> > I found a thread that had the same error with mine (in FS v.5.3) :
> >
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
> >
> > But the link to download 3dvolreg.afni doesn't work. Is this the same
> > 3dvolreg.afni for v.5.3 and v.6?
> >
> > Thanks,
> > Trinh
> >
> >
> >
> >
> > ___
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> --
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] missing 3volreg.afni

2015-12-22 Thread Thục Trinh

The link is fine. But when I click on the 3dvolreg file to get the
download, it failed with the error: "this webpage is not available"

2015-12-22 23:12 GMT+07:00 Douglas Greve :

> what happens when you click on it?
>
>
> On 12/22/15 9:28 AM, Thục Trinh wrote:
>
> Hi Douglas,
> It still does not work.
>
> 2015-12-21 23:29 GMT+07:00 Douglas N Greve :
>
>> that link works for me. Can you try again?
>>
>> On 12/20/2015 02:17 AM, Thục Trinh wrote:
>> > Hi FS experts,
>> >
>> > I'm working on my fMRI data using FSFAST v.6 tool. But the first step
>> > of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI
>> > command 3dvolreg.afni ". *
>> > I found a thread that had the same error with mine (in FS v.5.3) :
>> >
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
>> >
>> > But the link to download 3dvolreg.afni doesn't work. Is this the same
>> > 3dvolreg.afni for v.5.3 and v.6?
>> >
>> > Thanks,
>> > Trinh
>> >
>> >
>> >
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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Re: [Freesurfer] missing 3volreg.afni

2015-12-22 Thread Thục Trinh

Hi,
It comes up with this error:
 /freesurfer/bin/3dvolreg.afni: Exec format error. Wrong Architecture.
ERROR: 3dvolreg.afni
Invalid null command.

2015-12-23 7:59 GMT+07:00 Douglas Greve :

> Try this one
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/3dvolreg.afni
>
> On 12/22/15 7:56 PM, Thục Trinh wrote:
>
> The link is fine. But when I click on the 3dvolreg file to get the
> download, it failed with the error: "this webpage is not available"
>
> 2015-12-22 23:12 GMT+07:00 Douglas Greve :
>
>> what happens when you click on it?
>>
>>
>> On 12/22/15 9:28 AM, Thục Trinh wrote:
>>
>> Hi Douglas,
>> It still does not work.
>>
>> 2015-12-21 23:29 GMT+07:00 Douglas N Greve < 
>> gr...@nmr.mgh.harvard.edu>:
>>
>>> that link works for me. Can you try again?
>>>
>>> On 12/20/2015 02:17 AM, Thục Trinh wrote:
>>> > Hi FS experts,
>>> >
>>> > I'm working on my fMRI data using FSFAST v.6 tool. But the first step
>>> > of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI
>>> > command 3dvolreg.afni ". *
>>> > I found a thread that had the same error with mine (in FS v.5.3) :
>>> >
>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
>>> >
>>> > But the link to download 3dvolreg.afni doesn't work. Is this the same
>>> > 3dvolreg.afni for v.5.3 and v.6?
>>> >
>>> > Thanks,
>>> > Trinh
>>> >
>>> >
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
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>>
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Re: [Freesurfer] missing 3volreg.afni

2015-12-27 Thread Thục Trinh

My platform is centOS6.4 final 64bit.
3dvolreg.afni still works when I used FSv5.3. but when I update to FSv.6, I
cannot use the 3dvolreg.afni.

2015-12-24 4:29 GMT+07:00 Douglas Greve :

> what is your platform? Do you have AFNI installed and does it work? If so,
> you can copy the 3dvolreg to 3dvolreg.afni and it should work.
>
>
> On 12/23/15 1:22 AM, Thục Trinh wrote:
>
> Hi,
> It comes up with this error:
>  /freesurfer/bin/3dvolreg.afni: Exec format error. Wrong Architecture.
> ERROR: 3dvolreg.afni
> Invalid null command.
>
> 2015-12-23 7:59 GMT+07:00 Douglas Greve :
>
>> Try this one
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/3dvolreg.afni
>>
>> On 12/22/15 7:56 PM, Thục Trinh wrote:
>>
>> The link is fine. But when I click on the 3dvolreg file to get the
>> download, it failed with the error: "this webpage is not available"
>>
>> 2015-12-22 23:12 GMT+07:00 Douglas Greve < 
>> gr...@nmr.mgh.harvard.edu>:
>>
>>> what happens when you click on it?
>>>
>>>
>>> On 12/22/15 9:28 AM, Thục Trinh wrote:
>>>
>>> Hi Douglas,
>>> It still does not work.
>>>
>>> 2015-12-21 23:29 GMT+07:00 Douglas N Greve < 
>>> gr...@nmr.mgh.harvard.edu>:
>>>
>>>> that link works for me. Can you try again?
>>>>
>>>> On 12/20/2015 02:17 AM, Thục Trinh wrote:
>>>> > Hi FS experts,
>>>> >
>>>> > I'm working on my fMRI data using FSFAST v.6 tool. But the first step
>>>> > of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI
>>>> > command 3dvolreg.afni ". *
>>>> > I found a thread that had the same error with mine (in FS v.5.3) :
>>>> >
>>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
>>>> >
>>>> > But the link to download 3dvolreg.afni doesn't work. Is this the same
>>>> > 3dvolreg.afni for v.5.3 and v.6?
>>>> >
>>>> > Thanks,
>>>> > Trinh
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > ___
>>>> > Freesurfer mailing list
>>>> > Freesurfer@nmr.mgh.harvard.edu
>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>> --
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
>>>> Fax: 617-726-7422
>>>>
>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>> Outgoing:
>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>
>>>> ___
>>>> 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 
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>>>
>>>
>>>
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[Freesurfer] visualize fsaverage

2016-01-19 Thread Thục Trinh

Hello freesurfer experts,

I'm having a trouble with visualize the first level analysis output of
FSFAST on brain surface (fsaverage).  When I open tksurfer tool to look at
the contrast for the analysis on Right hemisphere space, the result display
the contrast on left hemisphere and vice versa when I want to display the
contrast on Left hemisphere space.  I already checked the registration
quality after run pre-processing and the results were quite good.
I hope you can help me to figure out this problem.

Thank you and have a nice day,
Trinh
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Re: [Freesurfer] visualize fsaverage

2016-01-19 Thread Thục Trinh

I checked on the different computer and it's normal. My platform is CentOS
6.4final, how can I fix this on my computer.

thanks,
trinh

2016-01-19 23:53 GMT+07:00 Douglas N Greve :

> I'm wondering if it is some kind of display issue. I notice the color
> scale is flipped upside down. Is there another computer you can test it
> on? What platform are you using?
>
> On 01/19/2016 09:20 AM, Thục Trinh wrote:
> > Hi Bruce,
> > I worked on my functional data, the command lines below,
> >
> >   * preproc-sess -s NCP140008_1  -fsd raw -stc down -surface fsaverage
> > lhrh  -fwhm 7 -per-run
> >
> >   * mkanalysis-sess  -fsd raw -stc down  -surface fsaverage lh -fwhm 7
> > -event-related  -nskip 1 -paradigm work.par -nconditions 3 -spmhrf
> > 0 -TR 3 -refeventdur 1 -polyfit 2 -analysis my-work.sm07.lh
> >  -per-run -force
> >
> >   * mkcontrast-sess -analysis my-work.sm07.lh -contrast con-v-base -a 1
> >
> >   * selxavg3-sess -s NCP140008_1  -analysis my-work.sm07.lh
> >
> > after finish this step, I run the command to visualize the output
> >
> >   * tksurfer-sess -s NCP140008_1 -analysis my-work.sm07.lh  -c con-v-base
> >
> > The output is attached
> >
> > Thank you,
> > Trinh
> >
> >
> > 2016-01-19 21:01 GMT+07:00 Bruce Fischl  > <mailto:fis...@nmr.mgh.harvard.edu>>:
> >
> > Hi Trinh
> >
> > we can't help you unless you send us your command lines and screen
> > output.
> >
> > cheers
> > Bruce
> >
> > On Tue, 19 Jan 2016, Thục Trinh wrote:
> >
> > Hello freesurfer experts,
> > I'm having a trouble with visualize the first level analysis
> > output of
> > FSFAST on brain surface (fsaverage).  When I open tksurfer
> > tool to look at
> > the contrast for the analysis on Right hemisphere space, the
> > result display
> > the contrast on left hemisphere and vice versa when I want to
> > display the
> > contrast on Left hemisphere space.  I already checked the
> > registration
> > quality after run pre-processing and the results were quite good.
> > I hope you can help me to figure out this problem.
> >
> > Thank you and have a nice day,
> > Trinh
> >
> >
> >
> >
> > ___
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> >
> >
> > The information in this e-mail is intended only for the person to
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> > addressed. If you believe this e-mail was sent to you in error and
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> > contains patient information, please contact the Partners
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> >
> >
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] mkanalysis-sess

2016-01-22 Thread Thục Trinh

Hello,

I am using mkanalysis-sess command to configure analysis and I have some
questions.

1, After run preproc-sess on raw data, why would we want to repeat all the
flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it
gonna effect to our f.nii if I input different value from the previous
preproc-sess command ?

2. -refeventdur: I read that if we have different duration of stimuli, we
can set the -refeventdur equal the mean of all stimuli durations. But in my
study, the duration of stimulus depends on the reaction time of subject, so
it's gonna be different for each subject. how can I manage that?

Thank you,
Trinh
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[Freesurfer] Paired analysis FSFAST

2016-02-06 Thread Thục Trinh

Hello,

I'm working on group analysis in fMRI activation using FSFAST. I tend to
test whether any significant changed in fMRI activation within group across
two time points ( pre-training vs post). I ran first level already.  I
still confuse about the concat data and the mri_glmfit command. Here are
the command lines, I'm wondering if it runs exactly what I want it to do.

--  idlist

Input NCP140005_1
Input NCP140005_2
Input NCP140012_1
Input NCP140012_2
Input NCP140071_1
Input NCP140071_2
Input NCP140079_1
Input NCP140079_2
Input NCP140082_1
Input NCP140082_2
Input NCP140543_1
Input NCP140543_2
Input NCP140556_1
Input NCP140556_2
Input NCP140558_1
Input NCP140558_2

-- concat data
isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow -o
group2

-- FSGD file

GroupDescriptorFile 1
Title Con-arrow Gr2
Class Defi
Input NCP140005 Defi
Input NCP140012 Defi
Input NCP140071 Defi
Input NCP140079 Defi
Input NCP140082 Defi
Input NCP140543 Defi
Input NCP140556 Defi
Input NCP140558 Defi

-- run glm analyisis

mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii  --fsgd
con-arrow_group2.fsgd --C mean.mat

-- content in matrix contrast
 C = [ 1 0 ]

Thank you,
Trinh
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Re: [Freesurfer] Cortical Segmentation

2014-12-16 Thread Thục Trinh


 SE8RECON.tar.gz
<https://docs.google.com/file/d/0B1_Gk_rrHt9jSVJfVV83WEd3NzA/edit?usp=drive_web>

 SE19RECON.tar.gz
<https://docs.google.com/file/d/0B1_Gk_rrHt9jU0V6NW5mRTRtNms/edit?usp=drive_web>

 SE20RECON.tar.gz
<https://docs.google.com/file/d/0B1_Gk_rrHt9jZEREaks2bTc2OE0/edit?usp=drive_web>
Hi Bruce,

They are all T1-w contrast but acquired with different pulse sequences and
resolution.

SE8: sagital T1 Flair, at resolution 1x.9375x.9375
SE19: Axial FSPGR 3D, at resolution: .4688x.4688x.4
SE20: Axial FSPGR Bravo, at resolution: .4688x.4688x.4

The data after run *-Recon-all *are in the attach file

2014-12-14 22:28 GMT+07:00 Bruce Fischl :
>
> Hi Trinh
>
> what was the difference between the acquisitions? There is no way for us
> to determine the underlying cause from just the inflated/aparc views. If
> you send us the MRI data and/or the 3 subject dirs we can take a look.
>
> cheers
> Bruce
>
>
>
> On Sun, 14 Dec 2014, Thục Trinh wrote:
>
>  Hello Freesurfer Experts,
>> Here is my procedure that I have a small problem on:
>>
>> I took MRI structure images on one subject, but used different Contrast. I
>> ran Recon-all command on those images to finalize the best quality between
>> them.
>>
>> After running tksurfer command to see the results of cortical
>> segmentation, one image of SE8 (subject's identified name), has
>> been completely segmented and almost perfectly smooth; however, at the
>> same
>> time, the others of the same subject seem the border lines to be messed
>> up.
>> May you please explain to me specifically about that and furthermore to
>> show
>> me how to correct it.
>>
>> The images are attached to this email.
>> Hope to hear your positive feedback asap.
>>
>> Thank you and Have a nice day.
>> Trinh Tran.
>> [cleardot.gif]
>>
>>
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[Freesurfer] Preproc-sess failed

[Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

Re: [Freesurfer] Preproc-sess failed

[Freesurfer] paradigm file

Re: [Freesurfer] paradigm file

[Freesurfer] White matter Error

Re: [Freesurfer] White matter Error

Re: [Freesurfer] tilted head

Re: [Freesurfer] White matter Error

[Freesurfer] wrong segmentation

Re: [Freesurfer] wrong segmentation

[Freesurfer] FS v.6.0

[Freesurfer] missing 3volreg.afni

Re: [Freesurfer] missing 3volreg.afni

Re: [Freesurfer] missing 3volreg.afni

Re: [Freesurfer] missing 3volreg.afni

Re: [Freesurfer] missing 3volreg.afni

[Freesurfer] visualize fsaverage

Re: [Freesurfer] visualize fsaverage

[Freesurfer] mkanalysis-sess

[Freesurfer] Paired analysis FSFAST

Re: [Freesurfer] Cortical Segmentation

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