009/fmc_vs does not exist. I've added a better error trap.
doug
Kathryn Devaney wrote:
Hello all,
I'm running into two errors running selxavg-sess, and I haven't seen them anywhere in the archives. I get the same errors in the stable and the dev enviroments.
I don't know if this is significant, but I have two versions of this data, one version was projfrac'd and the other was not. The non-projfrac data does not return the errors - I re-ran projfrac but got the same errors again.
Please let me know if you have any suggestions.
Thanks very much! Kathryn
The command that I used for projrac was:
cd <run_dir> mris_volsmooth --i fmc.bhdr --o fmc_vs.bhdr --projfrac-avg 0 1 .1 --fwhm 0 --reg ../register.dat
And here's the output for mkanalysis and selxavg:
whatever:color_orientation_20060403/mystudy% pwd /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy whatever:color_orientation_20060403/mystudy% mkanalysis-sess.new -sf sessid -df sesspar -motioncor -fsd bold -paradigm paradigm_color.par -dt blocked -mcextreg -polyfit 2 -gammafit 2.25 1.25 -TR 5.8 -nconditions 2 -timewindow 23.6 -funcstem fmc_vs -analysis subj27_color_volsmooth -force INFO: analysis subj27_color_volsmooth exists, but overwrite forced by user. /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403 Completed successfully whatever:color_orientation_20060403/mystudy% selxavg-sess -sf sessid -df sesspar -a subj27_color_volsmooth -noomnibus INFO: WhitenFlag = 0
selxavg-sess logfile is /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/log/selxavg-sess-bold-subj27_color_volsmooth-060427102037.log
/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403 Thu Apr 27 10:20:39 EDT 2006 INFO (color_orientation_20060403): RunList = 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047
/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/bold selxavg2 -TR 5.8 -parname paradigm_color.par -o subj27_color_volsmooth/h -i 005/fmc_vs -i 006/fmc_vs -i 007/fmc_vs -i 008/fmc_vs -i 009/fmc_vs -i 010/fmc_vs -i 011/fmc_vs -i 012/fmc_vs -i 013/fmc_vs -i 014/fmc_vs -i 015/fmc_vs -i 016/fmc_vs -i 017/fmc_vs -i 018/fmc_vs -i 019/fmc_vs -i 020/fmc_vs -i 021/fmc_vs -i 022/fmc_vs -i 023/fmc_vs -i 024/fmc_vs -i 025/fmc_vs -i 026/fmc_vs -i 027/fmc_vs -i 028/fmc_vs -i 029/fmc_vs -i 030/fmc_vs -i 031/fmc_vs -i 032/fmc_vs -i 033/fmc_vs -i 034/fmc_vs -i 035/fmc_vs -i 036/fmc_vs -i 037/fmc_vs -i 038/fmc_vs -i 039/fmc_vs -i 040/fmc_vs -i 041/fmc_vs -i 042/fmc_vs -i 043/fmc_vs -i 044/fmc_vs -i 045/fmc_vs -i 046/fmc_vs -i 047/fmc_vs -cfg /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg
-ipr 0.89690721666667
cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory --- Parsing Config File: /autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg
-gammafit 2.25 1.25 -timewindow 23.2 -prestim 0 -polyfit 2 -TER 5.8 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 Logfile is subj27_color_volsmooth/h_sxa.log matlab file is /tmp/sxa_17501.m ----------- Matlab file -------------- % Matlab file for selxavg2 Thu Apr 27 10:21:05 EDT 2006 % This file may be deleted % /tmp/sxa_17501.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '5.8', '-parname', 'paradigm_color.par', '-o', 'subj27_color_volsmooth/h', '-i', '005/fmc_vs', '-i', '006/fmc_vs', '-i', '007/fmc_vs', '-i', '008/fmc_vs', '-i', '009/fmc_vs', '-i', '010/fmc_vs', '-i', '011/fmc_vs', '-i', '012/fmc_vs', '-i', '013/fmc_vs', '-i', '014/fmc_vs', '-i', '015/fmc_vs', '-i', '016/fmc_vs', '-i', '017/fmc_vs', '-i', '018/fmc_vs', '-i', '019/fmc_vs', '-i', '020/fmc_vs', '-i', '021/fmc_vs', '-i', '022/fmc_vs', '-i', '023/fmc_vs', '-i', '024/fmc_vs', '-i', '025/fmc_vs', '-i', '026/fmc_vs', '-i', '027/fmc_vs', '-i', '028/fmc_vs', '-i', '029/fmc_vs', '-i', '030/fmc_vs', '-i', '031/fmc_vs', '-i', '032/fmc_vs', '-i', '033/fmc_vs', '-i', '034/fmc_vs', '-i', '035/fmc_vs', '-i', '036/fmc_vs', '-i', '037/fmc_vs', '-i', '038/fmc_vs', '-i', '039/fmc_vs', '-i', '040/fmc_vs', '-i', '041/fmc_vs', '-i', '042/fmc_vs', '-i', '043/fmc_vs', '-i', '044/fmc_vs', '-i', '045/fmc_vs', '-i', '046/fmc_vs', '-i', '047/fmc_vs', '-cfg', '/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/mystudy/subj27_color_volsmooth/analysis.cfg', '-ipr', '0.89690721666667'); if(r==0) fmri_touch('/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403/bold/subj27_color_volsmooth/selxavg.ok.17501'); end qoe;
------- matlab output --------------------
< M A T L A B > Copyright 1984-2003 The MathWorks, Inc. Version 6.5.1.199709 Release 13 (Service Pack 1) Aug 4 2003Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspblks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmasks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmex. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspdemos.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
>>>>>>>$Id: fast_selxavg.m,v 1.22.2.1 2006/04/06 22:31:16 greve >>>>>>> >>>>>>>
Exp $ Parsing Arguments Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 43 Input Volume List 1 005/fmc_vs 2 006/fmc_vs 3 007/fmc_vs 4 008/fmc_vs 5 009/fmc_vs 6 010/fmc_vs 7 011/fmc_vs 8 012/fmc_vs 9 013/fmc_vs 10 014/fmc_vs 11 015/fmc_vs 12 016/fmc_vs 13 017/fmc_vs 14 018/fmc_vs 15 019/fmc_vs 16 020/fmc_vs 17 021/fmc_vs 18 022/fmc_vs 19 023/fmc_vs 20 024/fmc_vs 21 025/fmc_vs 22 026/fmc_vs 23 027/fmc_vs 24 028/fmc_vs 25 029/fmc_vs 26 030/fmc_vs 27 031/fmc_vs 28 032/fmc_vs 29 033/fmc_vs 30 034/fmc_vs 31 035/fmc_vs 32 036/fmc_vs 33 037/fmc_vs 34 038/fmc_vs 35 039/fmc_vs 36 040/fmc_vs 37 041/fmc_vs 38 042/fmc_vs 39 043/fmc_vs 40 044/fmc_vs 41 045/fmc_vs 42 046/fmc_vs 43 047/fmc_vs Input Pardigm File List 1 005/paradigm_color.par 2 006/paradigm_color.par 3 007/paradigm_color.par 4 008/paradigm_color.par 5 009/paradigm_color.par 6 010/paradigm_color.par 7 011/paradigm_color.par 8 012/paradigm_color.par 9 013/paradigm_color.par 10 014/paradigm_color.par 11 015/paradigm_color.par 12 016/paradigm_color.par 13 017/paradigm_color.par 14 018/paradigm_color.par 15 019/paradigm_color.par 16 020/paradigm_color.par 17 021/paradigm_color.par 18 022/paradigm_color.par 19 023/paradigm_color.par 20 024/paradigm_color.par 21 025/paradigm_color.par 22 026/paradigm_color.par 23 027/paradigm_color.par 24 028/paradigm_color.par 25 029/paradigm_color.par 26 030/paradigm_color.par 27 031/paradigm_color.par 28 032/paradigm_color.par 29 033/paradigm_color.par 30 034/paradigm_color.par 31 035/paradigm_color.par 32 036/paradigm_color.par 33 037/paradigm_color.par 34 038/paradigm_color.par 35 039/paradigm_color.par 36 040/paradigm_color.par 37 041/paradigm_color.par 38 042/paradigm_color.par 39 043/paradigm_color.par 40 044/paradigm_color.par 41 045/paradigm_color.par 42 046/paradigm_color.par 43 047/paradigm_color.par Output Volume subj27_color_volsmooth/h TR 5.800000 TER 5.800000 Total Window 23.2 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 0 nSkip 0 InPlane Res 0.896907 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 1 2.25 1.25 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 ExtReg File mcextreg NExtReg 3 ExtRegOrthog 0 firstslice 0 nslices 26 nyqreg 0 SynthSeed = 0 Conditions Found (2): 1 2 Run 1: 8 7 Run 2: 8 7 Run 3: 8 7 Run 4: 8 7 Run 5: 8 8 Run 6: 8 8 Run 7: 8 8 Run 8: 8 8 Run 9: 8 8 Run 10: 8 8 Run 11: 8 8 Run 12: 8 8 Run 13: 8 8 Run 14: 8 8 Run 15: 8 8 Run 16: 8 8 Run 17: 8 8 Run 18: 8 8 Run 19: 8 8 Run 20: 8 8 Run 21: 8 8 Run 22: 8 8 Run 23: 8 8 Run 24: 8 8 Run 25: 8 8 Run 26: 8 8 Run 27: 8 8 Run 28: 8 8 Run 29: 8 8 Run 30: 8 8 Run 31: 8 8 Run 32: 8 8 Run 33: 8 8 Run 34: 8 8 Run 35: 8 8 Run 36: 8 8 Run 37: 8 8 Run 38: 8 8 Run 39: 8 8 Run 40: 8 8 Run 41: 8 8 Run 42: 8 8 Run 43: 8 8 Slice 0, 0.000334 -------------- First Pass (Accumulation), 0.006474 Run 1/43, 0.007439 Excluding 0 Points: Run 2/43, 1.23839 Excluding 0 Points: Run 3/43, 2.14573 Excluding 0 Points: Run 4/43, 3.051 Excluding 0 Points: Run 5/43, 3.97482 Excluding 0 Points: Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.)
In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at
line 35 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Divide by zero. (Type "warning off MATLAB:divideByZero" to suppress this warning.)
In
/autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/matlab/datafun/std.m at line 33 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 37 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.)
In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at
line 35 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Divide by zero. (Type "warning off MATLAB:divideByZero" to suppress this warning.)
In
/autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/matlab/datafun/std.m at line 33 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at line 37 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 Warning: Matrix is singular to working precision. (Type "warning off MATLAB:singularMatrix" to suppress this warning.)
In /usr/local/freesurfer/stable/fsfast/toolbox/fast_polytrendmtx.m at
line 47 In /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m at line 285 ??? Index exceeds matrix dimensions.
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fmri_par2scm.m On line 112 ==> c1(1) = Pulses(1);
Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 324 ==> Xfir = fmri_par2scm(par,Nc,SubSampRate*ntrs,TER,Nfir,TPS);
??? Undefined function or variable 'r'.
quiting matlab
ERROR: fast_selxavg() failed\n ERROR (/autofs/space/annecy_014/users/kdevaney/subj27/color_orientation_20060403): selxavg failed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer