Dear. Experts.
I appreciate your help in advance.
I also tried: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile
Then I got the error: ------------------------------------------------------------- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160308154755.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Tue Mar 8 15:47:56 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino 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.
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>> >> >> >>
sxa3pwd =
/home/jbang/Projects/replay/log
sxa3cmd =
/usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino -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 ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc (MRIread)
Error in ==> flac_customize at 87 mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
Could you please help? Before running this, I run preproc-sess.
Thank you.
Best, Ji Won
2016-03-08 14:41 GMT-05:00 Ji Won Bang kirstens03@gmail.com:
Dear. Freesurfer experts.
Hi.
I'm using freesurfer version 5.3.0.
I tried:
mkanalysis-sess -analysis retino -TR 2 -paradigm para.para -event-related -funcstem fmc -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force -fsd bold_retino -per-run -native -refeventdur 8
mkcontrast-sess -analysis retino -contrast HorVer -a 1 -c 2
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -nosmooth -per-run
selxavg-sess -s $SUBJECT -analysis retino -df sessdirfile -noomnibus
Then at the selxavg-sess process, I got the error:
INFO: WhitenFlag = 0
selxavg-sess logfile is /home/jbang/Projects/replay/log/log/selxavg-sess-bold_retino-retino-160308143510.log
/home/jbang/Projects/replay/epi/replay06 Tue Mar 8 14:35:10 EST 2016 ERROR: could not find volume ERROR:. Does it exist? (standard_in) 1: syntax error ERROR: could not find volume ERROR:. Does it exist? inplaneres TR INFO (replay06): RunList = 023 025 027 029
/home/jbang/Projects/replay/epi/replay06/bold_retino selxavg2 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg
--- Parsing Config File: /home/jbang/Projects/replay/log/retino/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: Flag 3 unrecognized. -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg ERROR (/home/jbang/Projects/replay/epi/replay06): selxavg failed
Could you please hlep what's going wrong?
Thank you very much!
Best, Ji Won