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>

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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