Hello, I know this problem has been discussed earlier, but I think in my case the source of the problem might be quite different. I'm running FS 5.3.0 and MATLAB R2011a on Ubuntu machine with 12 GB RAM. selxavg3-sess runs perfectly for both hemis, but I get the following error when trying to run it on subcortical volume:
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/marcel/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/marcel/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/marcel/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/2TB/SDT_MRI/FS Extension format = nii.gz 1 DC_vs_HC.mat 2 HI_vs_DC.mat 3 HI_vs_HC.mat 4 NAT_vs_PAL.mat 5 NAT_vs_PAT.mat 6 PAL_vs_NAT.mat 7 PAL_vs_PAT.mat nruns = 1 autostimdur =
outanadir = /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni Found 52644/537168 ( 9.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 851, nX = 19, DOF = 832 Saving X matrix to /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni/Xtmp.mat XCond = 31.0456 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500489 (t=0.097569) 2 -0.25 -0.255326 (t=0.427178) 3 0 -0.011955 (t=0.516085) 4 0.25 0.229273 (t=0.839369) 5 0.5 0.466983 (t=0.928175) AR1 Correction M: 0.0147777 1.03322 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 1120.98 Global In-Mask Mean = 1120.98 (983.432) Rescale Target = 100 RescaleFactor = 0.0892077 OLS Residual Pass run 1 t= 0.0 ??? Out of memory. Type HELP MEMORY for your options.
Error in ==> fast_selxavg3 at 489 rsserun = sum(rrun.^2);
I observed memory consuption with top(8) and noticed that around 11 GBs are eaten after about 30 second of running OLS residual pass. Do you think adding more memory to the PC would solve the problem, or is it some MATLAB/FS-related bug?
Best regards, Marcel
It is not a matlab problem per se, though their memory management is not great. This sometimes happens for the mni305 when you have a lot of time points in one run or many runs. How many runs and how many time points per run? And you are doing 2mm (the default) or 1mm? doug
On 6/13/13 2:19 PM, Marcel Falkiewicz wrote:
Hello, I know this problem has been discussed earlier, but I think in my case the source of the problem might be quite different. I'm running FS 5.3.0 and MATLAB R2011a on Ubuntu machine with 12 GB RAM. selxavg3-sess runs perfectly for both hemis, but I get the following error when trying to run it on subcortical volume:
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/marcel/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/marcel/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/marcel/freesurfer/matlab/MRIread.m
outtop = /media/2TB/SDT_MRI/FS Extension format = nii.gz 1 DC_vs_HC.mat 2 HI_vs_DC.mat 3 HI_vs_HC.mat 4 NAT_vs_PAL.mat 5 NAT_vs_PAT.mat 6 PAL_vs_NAT.mat 7 PAL_vs_PAT.mat nruns = 1 autostimdur =
outanadir = /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni Found 52644/537168 ( 9.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 851, nX = 19, DOF = 832 Saving X matrix to /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni/Xtmp.mat XCond = 31.0456 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500489 (t=0.097569) 2 -0.25 -0.255326 (t=0.427178) 3 0 -0.011955 (t=0.516085) 4 0.25 0.229273 (t=0.839369) 5 0.5 0.466983 (t=0.928175) AR1 Correction M: 0.0147777 1.03322 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 1120.98 Global In-Mask Mean = 1120.98 (983.432) Rescale Target = 100 RescaleFactor = 0.0892077 OLS Residual Pass run 1 t= 0.0 ??? Out of memory. Type HELP MEMORY for your options.
Error in ==> fast_selxavg3 at 489 rsserun = sum(rrun.^2);
I observed memory consuption with top(8) and noticed that around 11 GBs are eaten after about 30 second of running OLS residual pass. Do you think adding more memory to the PC would solve the problem, or is it some MATLAB/FS-related bug?
Best regards, Marcel
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Douglas Greve -
Marcel Falkiewicz