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 cjkeller@partners.org ckeller@nmr.mgh.harvard.edu
Hi Corey,
I just ran selxav3,
Check my log and output dir (both dof and mask.nii are created), it looks fine.
pratap
[galen:bold] (nmr-std-env) cd VvI_MK_Analysis/ [galen:VvI_MK_Analysis] (nmr-std-env) LS acfsegLUT.txt allvfix dof fsnr.nii fwhm.sum h.nii mask.nii omnibus rho1.nii rvar.nii acfseg.nii beta.nii fsnr2.nii fwhm.dat h.dat h-offset.nii meanfunc.nii rho1mn.nii rstd.nii X.mat [galen:VvI_MK_Analysis] (nmr-std-env) more dof 86
Log: [galen:S4_HR_LR18VvI] (nmr-std-env) selxavg3-sess -s rfa0413 -analysis VvI_MK_Analysis/ -overwrite -------------------------------------------------------------- selxavg3-sess logfile is /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/log/selxavg3-sess-bold-VvI_MK_Analysis-071116130312.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413 Fri Nov 16 13:03:13 EST 2007 anadir = /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_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.
>> >> >> >> /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/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. nruns = 1 autostimdur = 1
outanadir = /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis Found 56169/143360 (39.2) voxels in mask Creating Design Matrix Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. ntptot = 100, nX = 14, DOF = 86 XCond = 226.263 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.532209 (t=0.017135) 2 -0.25 -0.318684 (t=0.02182) 3 0 -0.120952 (t=0.02537) 4 0.25 0.0508019 (t=0.028981) 5 0.5 0.176664 (t=0.03252) AR1 Correction M: 0.20632 1.38585 Computing contrast matrices Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. 1 omnibus J= 8 eff = 1.4 vrf = 10.9642 vrfffx = 10.9642 r = 1.00 Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. 2 allvfix J= 1 eff = 0.8 vrf = 0.7544 vrfffx = 0.7544 r = 1.00 OLS Beta Pass run 1 t= 0.0 Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. Global In-Mask Mean = 691.858 Rescale Target = 100 RescaleFactor = 0.144538 OLS Residual Pass run 1 t= 0.0 Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. Whitening Computing whitening matrices seg 1 5617 nrho1 = -0.031 (t= 0.0) seg 2 5617 nrho1 = 0.105 (t= 0.1) seg 3 5617 nrho1 = 0.186 (t= 0.1) seg 4 5617 nrho1 = 0.254 (t= 0.1) seg 5 5617 nrho1 = 0.318 (t= 0.1) seg 6 5617 nrho1 = 0.382 (t= 0.2) seg 7 5617 nrho1 = 0.451 (t= 0.2) seg 8 5617 nrho1 = 0.529 (t= 0.2) seg 9 5617 nrho1 = 0.625 (t= 0.2) seg 10 5616 nrho1 = 0.794 (t= 0.2) GLS Beta Pass run 1 t= 0.0 Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. GLS Residual Pass run 1 t= 0.0 Loaded /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/014/VvI8.para as a par2 file. Found 0 zero-valued voxels Computing contrasts Starting contrasts omnibus J=8 ------------- Computing CES Magnitude allvfix J=1 ------------- Saving h.dat to /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/h.dat
>> ------------------------------------------
------------------------------------------- Computing FWHM ------------------------------------------- /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413 Fri Nov 16 13:03:45 EST 2007 /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI mri_concat /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/res/res-001.nii --o /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/res/all.nii ninputs = 1 Checking inputs nframestot = 100 Allocing output Writing to /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/res/all.nii /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI mri_fwhm --mask /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/mask.nii --i /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/res/all.nii --sum /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/fwhm.sum --dat /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/fwhm.dat voxelvolume 39.0625 mm3 Loading mask /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/mask.nii Search region is 56169 voxels = 2194101.776768 mm3 Polynomial detrending, order = 0 Detrending Computing spatial AR1 in volume. fMRIspatialAR1(): hit 45829 voxels ar1mn = (0.636386,0.628951,0.386435) colfwhm = 5.473086 rowfwhm = 5.403290 slicefwhm = 4.829978 outfwhm = 5.243374 reselvolume 142.835345 nresels 15361.056290 nvoxperresel 3.656584 Copying h.dat cp /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI/rfa0413/bold/VvI_MK_Analysis/h.dat VvI_MK_Analysis Started at Fri Nov 16 13:03:12 EST 2007 Ended at Fri Nov 16 13:03:51 EST 2007
selxavg3-sess completed
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, 2005To 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, 2005To 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, 2005To 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, 2005To 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, 2005To 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, 2005To 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 cjkeller@partners.org ckeller@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Keller, Corey J. -
Pratap Kunwar