Dear Marta, Devita and SPM
There are several memory variables to be adjusted and one hack to be
implemented to help run large numbers of files in SPM.
1) Adjust the MaxMem variable.
JOHN: THIS IS ALSO A PLEA TO MOVE MAXMEM FROM SPM_SPM TO SPM_DEFAULTS SO
THAT USERS CAN EASILY ADJUST THIS VALUE TO DEAL WITH DIFFERENT SIZE
ANALYSES. PLEASE 8-)
Anyway MaxMem is is one of the first lines after the help info in
spm_spm.m. Your current setting tells spm to load voxels in 512000 K chunks
(536 MB!). Because there are many other variables that may be large with
many images this is probably too big. I suggest trying 2^24 or even 2^20.
Understand that with loading smaller chunks the analysis will take longer
to run. To do this without affecting your site's installation of spm do the
following.
copy spm_spm.m to your home directory (/home/~user or whatever
it is)
Start matlab and spm99
type rmpath /home/~user
(This command removes your home directory from the
matlab path. If your home directory is not in the
matlab path
you'll get an error but don't worry about it).
type addpath /home/~user
(This command will now add back your home directory
as the first folder in the matlab path. Now matlab
will look
first in your come directory for any functions and
will use
your modified version of spm_spm.m first)
type path
(check that the path has been appropriately modified.
Your should see something like:
/home/~user
/matlabr11/toolbox/spm99
/matlabr11/OtherMatlabDirectories)
type clear functions (makes sure matlab rechecks all paths)
edit the spm_spm.m and change the MaxMem variable.
save and close the file
2) Don't set up all F-contrasts, particularly if your experiment has many
conditions. This will just take a long time to set up and matlab never
entirely clears all the memory it uses for this type of operation.
3) Hack- add preallocation of the XYZ matrix during the analysis. During
analysis spm_spm adds to a matrix called XYZ. This is a growing list voxel
locations to be saved. The way spm_spm is written it adds onto a matrix.
This is much less efficient and much slower than preallocating a matrix of
zeros, substituting the voxel values, and trimming the zeros at the end. I
have attached a modified version of spm_spm (version 2.37.1) that I have
hacked to do just this. See lines:
maxMem 341
preallocate XYZ 638
sub in voxels 1011
trim zeros 1173
The modification does not change any of the analysis (as far as I can tell)
so it can either be substituted for the current version of spm_spm.m or
placed in your home folder just as noted above. We have been able to run
analyses of > 8000 images (64x64x32) using these strategies.
Of course all the usual disclaimers apply to this modified version of
spm_spm: that there is no warranty or support, that it might give you
incorrect results, or that it might destroy your hard drive, your computer
or your life.
Regards,
Darren
At 03:40 PM 5/25/2001 +0200, you wrote:
>Dear SPMer's,
> I wrote some time ago but I haven't solved my problem.
>I think that my problem is related to the fact that I have a big single
>session with 3900 volumes.
>Is possible that my problems of "out of memory" derive from this??
>
>My MaxMem varialbe is just set as 2^29.
>Can I change the memory for a single session??
>
>
> I have a single session formed by 3600 images (8192 bytes each).
> The subject has done simple finger tapping with both hads.
> I've build a matrix design and estimate a model with this design
>matrix.
>
> SPM reads all the images, 3600/3600 but it is not able to complete the
> estimate. I've the following error:
>
>
> Saving SPMstats configuration : ...SPMcfg.mat
>saved
>
> Design reporting :
> ...done
>
> SPM99: spm_spm (v2.37) 03:25:34 -
> 24/03/2001
>
>
> =======================================================================
>
> Initialising design space :
> ...computing??? Error using ==> *
> Out of memory. Type HELP MEMORY for your options.
>
> Error in ==> C:\SPM99\spm99_updates\spm_filter.m
> On line 140 ==> y = K{s}.KL*y;
>
> Error in ==> C:\SPM99\spm_spm.m
> On line 440 ==> V = spm_filter('apply',xX.K,KVi');
>
> Error in ==> C:\SPM99\spm_fmri_spm_ui.m
> On line 619 ==> spm_spm(VY,xX,xM,F_iX0,Sess,xsDes);
>
> ??? Error while evaluating uicontrol Callback.
>
>
> Is possible that this error is related to the varialbe who sets memory
> of session???
> Can anybody tell me where can I set this variable in order to extend my
>
> memory session?
>
> Thanks
>
> Marta
>
>
>======================================
>
>Dr. Marta Maieron
>Dip. Scienze e Tecnologie Biomediche
>Università di Udine
>Piazzale Kolbe, 4
>33100 Udine
>Italy
>
>Phone: +39-0432-494360
>Fax: +39-0432-494301
