[pymvpa] Memory Error when Loading fMRI dataset

[Yaroslav Halchenko]

On Mon, 13 Jan 2014, Jason Ozubko wrote:

>    Hello,
>    I'm currently trying to setup my first MVPA analysis after working through
>    a few tutorials and I'm hitting a snag at the first stage, loading in the
>    data! �I've got a rather long experiment (~80 minutes, 2.2 s TR, broken
>    into about 5 sessions/runs). �I do some minimal preprocessing in SPM
>    before outputting 4D nii files that contain the functional data that I
>    want to use in my MVPA analyses.
>    My initial idea was to concatenate all the runs into 1 big .nii and then
>    load that in as a single dataset using fmri_dataset however when I try
>    this, I get a memory error (see the attached txt file for a full output)
>    I have since learned that python does not seem to crash if I try loading
>    in the runs individually (i.e., if I have 5 separate .nii files, each
>    containing functional data from a different run). �I am wondering, if I
>    loaded in the runs individually, and then I concatenated the loaded
>    datasets into one big dataset and then added the sa.targets and sa.chunks
>    properties appropriately, could I then proceed to the next steps of my
>    analysis and carry forward normally, or will there be issues with the fact
>    that I have concatenated the datasets together?

no -- concatenated datasets are as good.  But I have a concern about the
memory limit you have experienced:  most probably you would keep hitting
it again.  How much memory do you have available, and how big is the
actual dataset? (we still do not know dimensions to do algebra
ourselves here).  Also intersting is -- that big .nii, did it have the
same original datatype?

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik