In that case, you could break it up in to several shorter runs. It won't affect the stats much (probably help it), but it does make it a little more difficult to set up the data. If you want to do this, you would need to do something like this:
cd session/bold mv 001 001.big --> move the original data mkdir 001 002 003 004 --> create 4 folders mri_convert 001.big/f.nii.gz 001/f.nii.gz --fsubsample 0 1 99 --> first 200 time points mri_convert 001.big/f.nii.gz 002/f.nii.gz --fsubsample 200 1 299 ...
You will also need a paradigm file in each subdir. For 001, you can just cp 001.big/paradigmfile 001
For 002 003 004, it will need to be changed to reflect the new timing with something like cat 001.big/paradigmfile | awk '{print $1-200*2" "$2" "$3" "$4} > 002/paradigmfile cat 001.big/paradigmfile | awk '{print $1-400*2" "$2" "$3" "$4} > 003/paradigmfile cat 001.big/paradigmfile | awk '{print $1-600*2" "$2" "$3" "$4} > 004/paradigmfile The "2" in the "200*2" is the TR, change it if it is something different.
It does not matter if the paradigm files have events that are before the start of the "run" or after its end.
doug
ps. Adding more memory would fix it, but I don't know how much you would need to add
On 6/13/13 4:29 PM, Marcel Falkiewicz wrote:
Hello Doug, I've got only one run with approximately 800 timepoints. I'm doing the analysis in 2mm space.
Marcel
2013/6/13 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Douglas Greve