[Mne_analysis] Speeding up mne_make_movie

acgt2 at cam.ac.uk acgt2 at cam.ac.uk
Tue Jan 22 17:03:35 EST 2013
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Hi Alex,

I can confirm that creating-an-inverse-solution-and-morphing-to-average
using the python code is much faster than trying to do the same thing with
the mne_make_movie command or using the matlab functions when doing many
single trials.

Thanks for your suggestion,

Andy


-----Original Message-----
From: Alexandre Gramfort [mailto:gramfort at nmr.mgh.harvard.edu] 
Sent: 17 January 2013 21:43
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] Speeding up mne_make_movie

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-i
nverse-plot-morph-data-py

hope this helps,

Alex

On Thu, Jan 17, 2013 at 6:11 PM, <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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