Unfortunately encountered a problem in fs-fast stream during execution of
selxavg3-sess. Added a relevant part of the log file below:
>> >> >> >> >> >> >>
sxa3pwd =
/home/...removed...
>>
sxa3cmd =
/usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis
harm.sm0.mni305
>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# session02 ###############################
/home/...removed.../freesurfer_fMRT/session02
-------------------------
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/matlab/MRIread.m
-------------------------
outtop = /home/...removed.../freesurfer_fMRT
Extension format = nii.gz
1 stim-v-base.mat
nruns = 1
autostimdur =
outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305
Found 45239/537168 ( 8.4) voxels in mask
Creating Design Matrix
... creation time = 0.009 sec
DoMCFit = 1
ntptot = 100, nX = 8, DOF = 92
Saving X matrix to
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat
XCond = 444.207 (normalized)
Computing compensation for resdual AR1 bias
1 -0.5 -0.493933 (t=0.004964)
2 -0.25 -0.269463 (t=0.00648)
3 0 -0.0514275 (t=0.00734)
4 0.25 0.155364 (t=0.008221)
5 0.5 0.337574 (t=0.009058)
AR1 Correction M: 0.0769642 1.19552
Computing contrast matrices
OLS Beta Pass
run 1 t= 0.0
Global Mean 725.29
Global In-Mask Mean = 725.295 (694.97)
Rescale Target = 100
RescaleFactor = 0.137875
OLS Residual Pass
run 1 t= 0.0
Saving rho1
Smoothing ACF
/usr/local/freesurfer/bin/mri_fwhm --mask
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
--i
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
--o
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only
/usr/local/freesurfer/bin/mri_fwhm:
/usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
/usr/local/freesurfer/bin/mri_fwhm:
/usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9'
not found (required by /usr/local/freesurfer/bin/mri_fwhm)
ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
--i
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
--o
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
Seemingly a problem with "GLIBCXX_3.4.11". My OS is Lubuntu 13.04.
On Tue, 14 May 2013 08:28:05 +0200
Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> wrote:
> Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems.
> Also freeview runs without an error for the subject bert.
>
>
>
> On Mon, 13 May 2013 14:40:10 +0200
> Jörg Pfannmöller <pfannmo...@uni-greifswald.de> wrote:
>
> > Just for completeness, I refer to my first contribution:
> >
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Mon, 13 May 2013 13:58:30 +0200
> > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de> wrote:
> >
> > > Hello Nick,
> > >
> > > just installed and tested the BETA version. Up to now no problem
> > > encountered. Recon-all is just running as a test (using -use-gpu). OS is
> > > Lubuntu 13.04. I report on the segmentation as soon as it is finished.
> > >
> > > So long Joerg
> > >
> > > On Sun, 12 May 2013 22:41:25 -0400 (EDT)
> > > "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote:
> > >
> > > > Fedora 18, Ubuntu 13 and Gentoo 64 users,
> > > >
> > > > another beta of the upcoming v5.3 is available here:
> > > >
> > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
> > > >
> > > > this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
> > > > who wished to test that the segfault problem in v5.2 and the prior beta
> > > > v5.3 is fixed. Your help in testing this release is appreciated.
> > > >
> > > > Thanks,
> > > >
> > > > Nick
> > > >
> > > >
> > > >
> > > >
> > > > 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.
> > > >
> > >
> > >
> > > --
> > > Joerg Pfannmoeller <pfannmo...@uni-greifswald.de>
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > --
> > <pfannmo...@uni-greifswald.de>
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Joerg Pfannmoeller <pfannmo...@uni-greifswald.de>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Joerg Pfannmoeller <pfannmo...@uni-greifswald.de>
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