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 2003
Using 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
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