[pymvpa] Memory Error when Loading fMRI dataset

[Jason Ozubko]

Thanks for the advice everyone. I've tried loading the data in run-wise and
combining it and things seem to work fine!


On Tuesday, January 14, 2014, Nick Oosterhof wrote:

>
> On Jan 14, 2014, at 4:53 PM, Jason Ozubko wrote:
>
> > The dataset I'm working with has dimensions of 79x95x68 for each
> functional run, after being pre-processed from an original scan of
> 96x96x37.  There are 2151 functional runs in total across all 5 of my runs.
>  I am actually however, masking my data and so I only end up including
> about 950 voxels from each functional run.
> >
> > To me the error message seemed to indicate that I was running out of
> memory when I was loading the full dataset before any masking had occurred.
>  I wonder, if I load it in a piece meal fashion (1 run at a time) with the
> mask, after the data is loaded the masking should cut down on the number of
> voxels (and so overall memory signature) significantly, and so perhaps in
> the end I won't end up hitting a memory error once the data is loaded?
>
> That sounds plausible, as indeed first the full image is loaded and then
> the mask is applied - which reduces the required memory significantly after
> garbage collection.
>
> Thus indeed it may be better in your case to load the images run-wise, and
> then manually vstack them. Just be careful that the volume
> dimensions/positions match across the different runs, as with the manually
> stacking approach there is by default no check for this, unless you would
> use {h,v}stack with 'unique' as the second argument.
>
>
>
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