[Mne_analysis] Memory Error

[Diptyajit Das]

        External Email - Use Caution        

Hi alex,

Thanks for the suggestions. I tried with reduced source space('oct6'). I
can compute the resolution matrix but it doesn't match the size of the no.
of vertices of the original source space. Therefore, I am getting an error
while saving it as source estimate object .
Details:
original source space: 7503 locations (3 dipoles per each location)
Dimension of Inverse Matrix: (22509, 187)
Dimensions of resolution matrix: 22509 by 22509.
ValueError: Number of vertices (7503) and stc.shape[0] (22509) must match

However, I am expecting a resolution matrix with size of 7503*7503. Is the
resolution matrix being calculated each dipole location instead of taking
of normal of 3 components?? Any idea?

best,
Dip

On Thu, Jun 25, 2020 at 10:51 PM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

>         External Email - Use Caution
>
> hi,
>
> try reducing the size of your source space or find a machine with more RAM.
> It seems you need at least 25GB here.
>
> HTH
> Alex
>
> On Thu, Jun 25, 2020 at 9:04 PM Diptyajit Das <bmedasdiptyajit at gmail.com>
> wrote:
> >
> >         External Email - Use Caution
> >
> > Dear MNE users,
> >
> > I am trying to do something similar that has been done in this example:
> >
> https://mne.tools/stable/auto_examples/inverse/plot_psf_ctf_vertices.html#sphx-glr-auto-examples-inverse-plot-psf-ctf-vertices-py
> >
> > Except, I would like to compute my forward and Inverse operator with
> free orientation instead of being fixed or perpendicular to the cortical
> surface. However, I am getting this following error once I try to compute
> it. Is there any workaround to skip this memory error??
> >
> > Best,
> > Dip
> >
> > Error:
> > Traceback (most recent call last):
> >   File
> "/media/diptyajit/Elements/Pycharm_Aud_Cog/plot_psf_ctf_vertices.py", line
> 53, in <module>
> >     snr = 3.0
> >   File "<decorator-gen-313>", line 21, in make_inverse_resolution_matrix
> >   File
> "/home/diptyajit/anaconda3/lib/python3.7/site-packages/mne/minimum_norm/resolution_matrix.py",
> line 60, in make_inverse_resolution_matrix
> >     resmat = invmat.dot(leadfield)
> > MemoryError: Unable to allocate array with shape (56310, 56310) and data
> type float64
> >
> >
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