[Freesurfer] problem fast_selxavg3b
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 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] problem fast_selxavg3b
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 20.00 --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 20.00 --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 : > 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
Re: [Freesurfer] problem fast_selxavg3b
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.
Re: [Freesurfer] problem fast_selxavg3b
Thanks Doug! I have another question: We did the fsfast analysis some time ago before we updated freesurfer version with fast_selxavg3. Now we want to analyse additional persons. Do you think it is comparable or is it better to re-do the analysis for all persons with fast_selxavg3b instead of 13 persons with fast_selxavg3 and 2 persons with fast_selxavg3b? Thanks in advance, Desiree Am 29.09.2015 um 15:34 schrieb Douglas Greve: > 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
Re: [Freesurfer] problem fast_selxavg3b
Dear freesurfer experts, I included the new function 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 20.00 --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 20.00 --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 : > 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
Re: [Freesurfer] problem fast_selxavg3b
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 20.00 --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 20.00 --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 : > >> 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
Re: [Freesurfer] problem fast_selxavg3b
It is never good to mix versions, so I would re-do it. On 9/29/15 1:45 PM, Desiree Thielemann wrote: > Thanks Doug! > > I have another question: We did the fsfast analysis some time ago before > we updated freesurfer version with fast_selxavg3. Now we want to analyse > additional persons. Do you think it is comparable or is it better to > re-do the analysis for all persons with fast_selxavg3b instead of 13 > persons with fast_selxavg3 and 2 persons with fast_selxavg3b? > > Thanks in advance, > Desiree > > Am 29.09.2015 um 15:34 schrieb Douglas Greve: >> 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
Re: [Freesurfer] problem fast_selxavg3b
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 20.00 --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 20.00 --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 : >> >>> 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 >>
Re: [Freesurfer] problem fast_selxavg3b
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 20.00 --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 20.00 --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 : >>> 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.harvar
