[Mne_analysis] Memory Error
alexandre.gramfort at inria.fr
Mon Jun 29 16:20:27 EDT 2020
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it could be a bug. Can you open an issue so we can have a look at it?
On Fri, Jun 26, 2020 at 3:05 PM Diptyajit Das <bmedasdiptyajit at gmail.com> wrote:
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> 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 .
> 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 (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?
> On Thu, Jun 25, 2020 at 10:51 PM Alexandre Gramfort <alexandre.gramfort at inria.fr> wrote:
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>> try reducing the size of your source space or find a machine with more RAM.
>> It seems you need at least 25GB here.
>> On Thu, Jun 25, 2020 at 9:04 PM Diptyajit Das <bmedasdiptyajit at gmail.com> wrote:
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>> > 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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