[Mne_analysis] Speeding up mne_make_movie

[Alexandre Gramfort]

hi Andy,

it's likely that my matlab code for morphing is too naive for such a use case.
The python code is likely to be much more efficient (including
parallel computation)
I would give it a try.

here is an example of stc morphing in python:

http://martinos.org/mne/auto_examples/inverse/plot_morph_data.html#example-inverse-plot-morph-data-py

hope this helps,

Alex

On Thu, Jan 17, 2013 at 6:11 PM, A Thwaites <acgt2 at cam.ac.uk> wrote:
> Hi MNE-ers
>
>
>
> I am using mne_make_movie (mne version 2.7.3) to simultaneously apply an
> inverse operator to my sensor data, and morph the data to an ‘average’ brain
> using pre-computed morph maps. This works fine, but unfortunately I am doing
> this for 500 single trials, and for 20 subjects, and mne_make_movie applies
> the operator very slowly, to every millisecond (each trial is 2500 ms, and I
> can’t temporally downsample using --tstep as I need this high sample rate).
> In order to speed things up I was going to first use the
> mne_ex_compute_inverse matlab command  (as this seems to create the stcs a
> lot quicker) and then morph this stc data to the average using the matlab
> function ‘mne_morph_data’. The only problem is that mne_morph_data.m is very
> slow  (specifically lines 39-49) – indeed it seems much, much slower than
> the equivalent morphing step in mne_make_movie – largely cancelling out any
> gains made using mne_ex_compute_inverse! I suppose this might be something
> to do with matlab – in which case, is there a faster morphing function
> somewhere else I can call, for instance from the command line (ie not
> through mne_make_movie)? Or should I be abandoning the command line/matlab
> environment altogether, and use the python versions for all these commands
> (ie. mne.morph_data_precomputed?) (although I don’t know python so would
> rather avoid this for the present).
>
>
>
> Thanks for any help,
>
>
>
> Andy
>
>
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