Hi all,
I'm running into some problems using the selxavg3-sess command. Previously I
ran into a memory issue with matlab while running this command. However, when I
run the selxavg-sess command, the analysis completes successfully. This wasn't
an issue until I started averaging subjects. It appears that selxavg-sess
doesn't create the dof and mask and other files needed for the isxconcat-sess
command. Any suggestions? Thanks. Below is my code for selxavg3-sess and
selxavg-sess.
Best,
Corey
SELXAVG3
dgow:jsegawa[134] selxavg3-sess -sf sessid03 -df sesspar -analysis
simple_v_complex -overwrite
--------------------------------------------------------------
selxavg3-sess logfile is
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/log/selxavg3-sess-bold-sim
ple_v_complex-071116113229.log
--------------------------------------------------------------
-------------------------------------------
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003
Fri Nov 16 11:32:29 EST 2007
anadir =
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simple_v_complex
analysis simple_v_complex alread exists for PROZ06003
... reanalyzing (deleting old analysis)
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> >>
/usr/local/freesurfer/stable4/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v
1.55.2.1 2007/09/27 15:25:58 greve Exp $
outtop = /autofs/space/multnomah_003/users/gow/PROZ06/MRI
Extension format = nii
UseFloat = 0
INFO: acfbins is not set, setting to 10
INFO: mask is not set, setting to brain
1 allvres.mat
2 omnibus.mat
3 zallvres.mat
4 zomnibus.mat
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
nruns = 3
autostimdur =
outanadir =
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simple_v_complex
Found 41527/110592 (37.5) voxels in mask
Creating Design Matrix
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/011/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/012/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
ntptot = 1242, nX = 24, DOF = 1218
XCond = 56.8839 (normalized)
Computing compensation for resdual AR1 bias
1 -0.5 -0.493483 (t=16.1468)
2 -0.25 -0.248851 (t=46.0564)
3 0 -0.00487321 (t=48.3458)
4 0.25 0.237796 (t=78.3629)
5 0.5 0.477198 (t=94.7002)
AR1 Correction M: 0.00663368 1.02963
Computing contrast matrices
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
1 allvres J= 9 eff = 7.7 vrf = 69.6671 vrfffx = 69.2443 r = 1.01
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
2 omnibus J=18 eff = 11.1 vrf = 200.1014 vrfffx = 198.7246 r = 1.01
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
3 zallvres J= 9 eff = 7.7 vrf = 69.6671 vrfffx = 69.2443 r = 1.01
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
4 zomnibus J=18 eff = 11.1 vrf = 200.1014 vrfffx = 198.7246 r = 1.01
OLS Beta Pass
run 1 t= 0.0
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
run 2 t= 5.3
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/011/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
run 3 t=10.4
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/012/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
Global In-Mask Mean = 542.984
Rescale Target = 1000
RescaleFactor = 1.84167
OLS Residual Pass
run 1 t= 0.0
Loaded
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par
as a par2 file.Ignoring duration for FIR model
Ignoring duration for FIR model
??? Out of memory. Type HELP MEMORY for your options.
Error in ==> fast_selxavg3 at 417
rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun;
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
SELXAVG
dgow:jsegawa[132] selxavg-sess -sf sessid03 -df sesspar -analysis
simple_v_complex
INFO: WhitenFlag = 0
--------------------------------------------------------------
selxavg-sess logfile is
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/log/selxavg-sess-bold-simp
le_v_complex-071116111716.log
--------------------------------------------------------------
-------------------------------------------
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003
Fri Nov 16 11:17:17 EST 2007
INFO (PROZ06003): RunList = 010 011 012
--------------------------------------------------------
/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold
selxavg2 -TR 2.8000 -parname parfile1.par -o simple_v_complex/h -i 010/fmc -i
011/fmc -i 012/fmc -cfg
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis.
cfg -ipr 3.125 -pomnibus simple_v_complex/omnibus/fsig -fomnibus
simple_v_complex/omnibus/f
--------------------------------------------------------
here
--- Parsing Config File:
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis.
cfg ----
-timewindow 25.2 -prestim 0 -polyfit 1 -TER 2.8 -nskip 0 -fwhm 0 -rescale 1000
Logfile is simple_v_complex/h_sxa.log
matlab file is /tmp/sxa_31431.m
----------- Matlab file --------------
% Matlab file for selxavg2 Fri Nov 16 11:17:21 EST 2007
% This file may be deleted
% /tmp/sxa_31431.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.8000', '-parname', 'parfile1.par', '-o',
'simple_v_complex/h', '-i', '010/fmc', '-i', '011/fmc', '-i', '012/fmc', '-cfg',
'/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis
.cfg', '-ipr', '3.125', '-pomnibus', 'simple_v_complex/omnibus/fsig',
'-fomnibus', 'simple_v_complex/omnibus/f');
if(r==0)
fmri_touch('/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simp
le_v_complex/selxavg.ok.31431');
end
qoe;
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40.2.1 2007/10/05 21:10:30 greve Exp $
Parsing Arguments
RescaleTarget = 1000
UseMRIread = 1, ext = nii
Checking Parameters
nslices = 27
AutoStimDur: 0
StimDur:
Number of Runs: 3
Input Volume List
1 010/fmc
2 011/fmc
3 012/fmc
Input Pardigm File List
1 010/parfile1.par
2 011/parfile1.par
3 012/parfile1.par
Output Volume simple_v_complex/h
F Omnibus Volume simple_v_complex/omnibus/f
Sig Omnibus Volume simple_v_complex/omnibus/fsig
TR 2.800000
TER 2.800000
Total Window 25.2
PreStim Window 0
Remove Baseline 1
Remove Trend 0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 3.125
FWHM 0
Hanning Radius 0
Time Offset 0
GammaFit 0
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
firstslice 0
nslices 27
nyqreg 0
SynthSeed = 0
Conditions Found (2): 1 2
Run 1: 120 120
Run 2: 120 120
Run 3: 120 120
Slice 0, 5.2e-05 --------------
First Pass (Accumulation), 0.000607
Run 1/3, 0.001506
Excluding 0 Points:
Loading 010/fmc
Run 2/3, 3.67712
Excluding 0 Points:
Loading 011/fmc
Run 3/3, 6.96143
Excluding 0 Points:
Loading 012/fmc
Second Pass (Residual Error Estimation), 10.0999
Paradigm Condition: 51.2312
Var Reduction Range: 197.495 200.118 204.056
Computing hhat
Run 1/3, 10.1504
Excluding 0 Points:
Run 2/3, 10.4904
Excluding 0 Points:
Run 3/3, 10.8313
Excluding 0 Points:
Saving offset to simple_v_complex/h-offset_000.bfloat
INFO: performing FTest on omnibus
NOTE: if this hangs, try running selxavg-sess
with the -noomnibus flag.
Using MRIread(), which can slow things down.
Slice 1, 11.5265 --------------
Slice 2, 13.3047 --------------
Slice 3, 15.0746 --------------
Slice 4, 16.8374 --------------
Slice 5, 18.615 --------------
Slice 6, 20.4063 --------------
Slice 7, 22.2817 --------------
Slice 8, 24.2111 --------------
Slice 9, 26.0804 --------------
Slice 10, 27.9649 --------------
Slice 11, 29.8879 --------------
Slice 12, 31.8154 --------------
Slice 13, 33.7548 --------------
Slice 14, 35.6677 --------------
Slice 15, 37.6064 --------------
Slice 16, 39.4877 --------------
Slice 17, 41.5613 --------------
Slice 18, 43.5031 --------------
Slice 19, 45.4728 --------------
Slice 20, 47.4043 --------------
Slice 21, 49.4282 --------------
Slice 22, 51.3414 --------------
Slice 23, 53.2732 --------------
Slice 24, 55.1614 --------------
Slice 25, 57.0814 --------------
Slice 26, 59.1151 --------------
INFO: saving meta to simple_v_complex/X.mat
Done 64.2836
>> >> quiting matlab
------------------------------------------
Fri Nov 16 11:18:35 EST 2007
selxavg2: finished
$Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $
cmtxfile
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/allvres
nconds 2, wcond
ndelays 9, wdelay
ndelays 9, wpsa
sumconds 1
sumdelays 0
nircorr 0
TER 2.8
rdelta
rtau
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> Normalizing contrast matrix
>> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $
cmtxfile
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/omnibus
nconds 2, wcond
ndelays 9, wdelay
ndelays 9, wpsa
sumconds 0
sumdelays 0
nircorr 0
TER 2.8
rdelta
rtau
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> Normalizing contrast matrix
>> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $
cmtxfile
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/zallvres
nconds 2, wcond
ndelays 9, wdelay
ndelays 9, wpsa
sumconds 1
sumdelays 0
nircorr 0
TER 2.8
rdelta
rtau
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> Normalizing contrast matrix
>> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $
cmtxfile
/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/zomnibus
nconds 2, wcond
ndelays 9, wdelay
ndelays 9, wpsa
sumconds 0
sumdelays 0
nircorr 0
TER 2.8
rdelta
rtau
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Adding MNE Toolbox...
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> Normalizing contrast matrix
>> >> >> >> >> >> >> >> Started at Fri Nov 16 11:17:16 EST 2007
Ended at Fri Nov 16 11:18:47 EST 2007
COMPLETED SUCCESSFULLY
--------------------
Corey Keller
Epilepsy Unit
Clinical Research Coordinator
Massachusetts General Hospital
VBK 830, 55 Fruit Street
Boston, MA 02114
Phone 802.578.6292
Email [EMAIL PROTECTED]
[EMAIL PROTECTED]
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
