Dear. Freesurfer experts.
Hi. I'm trying retinotopy analysis using freesurfer version 5.3.0.
I'm having a problem when running selxavg3-sess...
Could you please help me with this issue?
I have 3 runs under bold_retino and all 3 scans have the same dimension..
The command line that I entered are:
mkanalysis-sess -analysis retino.lh -TR 2 -paradigm para.para -event-related -funcstem fmcpr.sm0.self.lh -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -nuisreg mcprextreg 3 -force -fsd bold_retino -per-run -surface self lh -refeventdur 8
mkcontrast-sess -analysis retino.lh -contrast HorVer -a 1 -c 2 mkcontrast-sess -analysis retino.lh -contrast UpperLower -a 3 -c 4
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-run -force -surface self lhrh -fwhm 0
selxavg3-sess -s $SUBJECT -analysis retino.lh -df sessdirfile
Then I get the error:
Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino.lh-160310164355.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Thu Mar 10 16:43:56 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
>> >> >> >>
sxa3pwd =
/home/jbang/Projects/replay/log
sxa3cmd =
/usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino.lh -df sessdirfile
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# replay06 ############################### /home/jbang/Projects/replay/epi/replay06 ------------------------- $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/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 3 autostimdur =
outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh Found 140089/148112 (94.6) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 360, nX = 22, DOF = 338 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/Xtmp.mat XCond = 200.812 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500111 (t=0.013194) 2 -0.25 -0.270166 (t=0.024429) 3 0 -0.0463709 (t=0.035203) 4 0.25 0.166079 (t=0.04517) 5 0.5 0.354234 (t=0.055571) AR1 Correction M: 0.0689761 1.16382 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 862.23 run 2 t= 2.0 Global Mean 864.13 run 3 t= 4.1 Global Mean 864.40 Global In-Mask Mean = 863.588 (889.887) Rescale Target = 100 RescaleFactor = 0.115796 OLS Residual Pass run 1 t= 0.0 Saving rho1 run 2 t= 3.4 Saving rho1 run 3 t= 7.1 Saving rho1 Smoothing ACF /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/ /usr/local/freesurfer//bin/mris_fwhm: /usr/local/matlab.r2009a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer//bin/mris_fwhm)
ERROR: /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/
ERROR: fast_selxavg3() failed\n
I'm getting confused what's causing this issue.
Please help!
I appreciate your advice in advance.
Thanks, Ji Won