Dear freesurfer experts,
I included the new function fast_selxavg3b but I got another problem:
First error:
/opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
ans =
127
Second error with another server running the analyses:
/opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol?
Do you have any suggestions how to solve the problem?
Best regard, Desiree
ERROR: fast_selxavg3() failed\n
Zitat von Douglas Greve greve@nmr.mgh.harvard.edu:
oops, sorry, that did not make it into the distribution. You can get it here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
thanks doug
On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
Dear members of the freesurfer mailing list,
I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to analyse mri data with fs-fast. I did the preprocessing and used the function mkanalysis-sess and mkcontrast-sess without any problems. I tried to run the function selxavg3-sess next and it stopped with the error message:
>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
/opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m /opt/freesurfer/matlab/MRIread.m
>> ??? Undefined function or method 'fast_selxavg3b' for input
arguments of type
'char'.
ERROR: fast_selxavg3() failed\n
I looked for the function fast_selxavg3b in matlab. Unfortunatly only the function fast_selxavg3 is included in the fsfast/toolbox. By trying to use the function fast_selxavg3, it recommand me to use fast_selxavg3b. I could not find the function in the internet.
Do you have any suggestions what to do?
Best regards, Desiree
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I don't think it is a matlab problem. We call some binaries from inside matlab, and the problem is with those. It looks like the version of FS does not match your operating system or that you are missing a library. Maybe Zeke can help sort it out. doug
On 10/5/15 2:31 AM, Desiree Thielemann wrote:
Dear freesurfer experts,
I included the new function fast_selxavg3b but I got another problem:
First error:
/opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
ans =
127Second error with another server running the analyses:
/opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol?
Do you have any suggestions how to solve the problem?
Best regard, Desiree
ERROR: fast_selxavg3() failed\n
Zitat von Douglas Greve greve@nmr.mgh.harvard.edu:
oops, sorry, that did not make it into the distribution. You can get it here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
thanks doug
On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
Dear members of the freesurfer mailing list,
I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to analyse mri data with fs-fast. I did the preprocessing and used the function mkanalysis-sess and mkcontrast-sess without any problems. I tried to run the function selxavg3-sess next and it stopped with the error message:
>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
/opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m /opt/freesurfer/matlab/MRIread.m
>>> ??? Undefined function or method 'fast_selxavg3b' for input
arguments of type
'char'.
ERROR: fast_selxavg3() failed\n
I looked for the function fast_selxavg3b in matlab. Unfortunatly only the function fast_selxavg3 is included in the fsfast/toolbox. By trying to use the function fast_selxavg3, it recommand me to use fast_selxavg3b. I could not find the function in the internet.
Do you have any suggestions what to do?
Best regards, Desiree
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I have seen errors that look like the error below (i.e. GLIBCXX_3.4.15) when their is an incompatibility between the OS, matlab, and the compiled binary. Looking at your path to matlab I see "/opt/matlab/R2010b". Thats pretty old.
Doug, I recall you telling me these binaries are compiled against matlab 8.3 (R2014a)? Perhaps Desiree should use that version.
-Zeke
On 10/05/2015 07:32 PM, Douglas Greve wrote:
I don't think it is a matlab problem. We call some binaries from inside matlab, and the problem is with those. It looks like the version of FS does not match your operating system or that you are missing a library. Maybe Zeke can help sort it out. doug
On 10/5/15 2:31 AM, Desiree Thielemann wrote:
Dear freesurfer experts,
I included the new function fast_selxavg3b but I got another problem:
First error:
/opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz --i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz --o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
ans =
127Second error with another server running the analyses:
/opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol?
Do you have any suggestions how to solve the problem?
Best regard, Desiree
ERROR: fast_selxavg3() failed\n
Zitat von Douglas Greve greve@nmr.mgh.harvard.edu:
oops, sorry, that did not make it into the distribution. You can get it here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
thanks doug
On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
Dear members of the freesurfer mailing list,
I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to analyse mri data with fs-fast. I did the preprocessing and used the function mkanalysis-sess and mkcontrast-sess without any problems. I tried to run the function selxavg3-sess next and it stopped with the error message:
>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m /opt/freesurfer/matlab/MRIread.m >>>> ??? Undefined function or method 'fast_selxavg3b' for input arguments of type
'char'.
ERROR: fast_selxavg3() failed\n
I looked for the function fast_selxavg3b in matlab. Unfortunatly only the function fast_selxavg3 is included in the fsfast/toolbox. By trying to use the function fast_selxavg3, it recommand me to use fast_selxavg3b. I could not find the function in the internet.
Do you have any suggestions what to do?
Best regards, Desiree
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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I don't think they are using the compiled version of selxavg. Rather, the matlab script makes a unix call to run an FS binary. I think this would happen for any binary. Desiree, can you run that command (mris_fwhm) outside of matlab to see if it runs?
On 10/06/2015 10:21 AM, Z K wrote:
Hello,
I have seen errors that look like the error below (i.e. GLIBCXX_3.4.15) when their is an incompatibility between the OS, matlab, and the compiled binary. Looking at your path to matlab I see "/opt/matlab/R2010b". Thats pretty old.
Doug, I recall you telling me these binaries are compiled against matlab 8.3 (R2014a)? Perhaps Desiree should use that version.
-Zeke
On 10/05/2015 07:32 PM, Douglas Greve wrote:
I don't think it is a matlab problem. We call some binaries from inside matlab, and the problem is with those. It looks like the version of FS does not match your operating system or that you are missing a library. Maybe Zeke can help sort it out. doug
On 10/5/15 2:31 AM, Desiree Thielemann wrote:
Dear freesurfer experts,
I included the new function fast_selxavg3b but I got another problem:
First error:
/opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
--i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
--o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann /opt/freesurfer/bin/mris_fwhm: symbol lookup error: /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
ERROR: /opt/freesurfer/bin/mris_fwhm --mask /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
--i /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
--o /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
ans =
127Second error with another server running the analyses:
/opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm) /opt/freesurfer/bin/mris_fwhm: /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
The problem seems to be the version of matlab. Which version would you suggest to use while using the function fast_selxavg3b? And why is there an undefined symbol?
Do you have any suggestions how to solve the problem?
Best regard, Desiree
ERROR: fast_selxavg3() failed\n
Zitat von Douglas Greve greve@nmr.mgh.harvard.edu:
oops, sorry, that did not make it into the distribution. You can get it here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
thanks doug
On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
Dear members of the freesurfer mailing list,
I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to analyse mri data with fs-fast. I did the preprocessing and used the function mkanalysis-sess and mkcontrast-sess without any problems. I tried to run the function selxavg3-sess next and it stopped with the error message:
>>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m > /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m > /opt/freesurfer/matlab/MRIread.m >>>>> ??? Undefined function or method 'fast_selxavg3b' for input > arguments of type
'char'.
> ------------------------------------------
ERROR: fast_selxavg3() failed\n
I looked for the function fast_selxavg3b in matlab. Unfortunatly only the function fast_selxavg3 is included in the fsfast/toolbox. By trying to use the function fast_selxavg3, it recommand me to use fast_selxavg3b. I could not find the function in the internet.
Do you have any suggestions what to do?
Best regards, Desiree
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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freesurfer@nmr.mgh.harvard.edu
-
Desiree Thielemann -
Douglas Greve -
Douglas N Greve
-
Z K