[Mne_analysis] make non reg/meg movie

[Eric Larson]

Sorry for not mentioning this earlier, you can also use this MATLAB
function (which comes bundled with the MNE-C tools):

https://github.com/mne-tools/mne-matlab/blob/master/matlab/mne_write_stc_file.m

It looks like your code is quite close, I'm not sure why it isn't working.
Maybe try the above file. Also, make sure you write both -lh and -rh stc
files, and have the proper number of vertices for the subject of interest
(for each hemisphere).

Eric


On Fri, Oct 3, 2014 at 2:21 PM, Gregory Kirk <gkirk at wisc.edu> wrote:

> Hi
>
> seemed to follow the format of the python script and wrote a matlab file
> fid=fopen('var-lh.stc','w');
> tmin = 1;
> tstep = 2;
> load my_var
> sz = size(my_var)
>  nvert=sz(1);
> ntime = sz(2);
> samp_rate = tstep*1000;
>
> fwrite(fid,tmin,'float32');
> fwrite(fid,samp_rate,'float32');
> fwrite(fid,nvert,'uint32');
> verts = [0:nvert-1];
> fwrite(fid,verts,'uint32');
> fwrite(fid,ntime,'uint32');
> fwrite(fid,my_var,'float32');
>
>  mne_make_movie --stcin var --mov test.mov
>
> mne_make_movie seems to think t has no verticies
>
> mne_make_movie version 1.34 compiled at Dec 21 2009 19:48:23
> Create movies and tif, rgb, jpeg, png, or w files using a precomputed
> inverse operator decomposition
>
> stc input file : var
> mov file output : test.mov
> width x height : 600 x 400
> QuickTime quality : 80
>  The input stc file will be assumed to contain current expectation value
> data
> Subject : 001_S1
> Visualization surface : inflated
>  Process both hemispheres
> Magnification factor : 1.00
> Thresholding:
>  fthresh : 8.00
>  fmid : 15.00
>  fslope : 0.20
>  fmax : 20.00
>
> -------------------------------------------------------------------
>
> 600 x 400 off-screen rendering initialized.
> Selected view called 'lat'
>
> -------------------------------------------------------------------
>
> No vertices in stc file var-lh.stc
>
>
>
>
> On 10/02/14, Eric Larson  wrote:
> > If you&#39;re comfortable with Python, then PySurfer will allow you to
> directly plot arbitrary data vectors on the cortical surface. Should be
> pretty easy for your use case.
> >
> > If you want to stick with Bash, then you can get the STC format spec
> from looking at the mne-python code for `SourceEstimate.save`, which calls
> `_write_stc`:
> >
> >
> >
> https://github.com/mne-tools/mne-python/blob/master/mne/source_estimate.py#L72
> >
> >
> >
> > I don&#39;t think you need to supply the `--inv`, `--meas`, or `--set`
> parameters to `mne_make_movie` if you provide `--stcin` (since those other
> parameters are basically used to create a STC in memory). You&#39;ll
> probably also need to specify the `--subject` and the output type (e.g.
> `--mov`). The following command works on my system:
> >
> >
> > mne_make_movie --stcin test-fsaverage-lh.stc --mov test.mov --subject
> fsaverage
> >
> >
> >
> > Eric
> >
> >
> >
> >
> > On Thu, Oct 2, 2014 at 2:21 PM, Gregory Kirk <
> Mne_analysis at nmr.mgh.harvard.edu <gkirk at wisc.edu')" target="1">
> gkirk at wisc.edu> wrote:
> >
> > > Hi,
> > >
> > > i recently posted to free surfer list and was invited to post to this
> list as it seems the men may be the best way
> > > for me to accomplish my task.
> > >
> > >
> > > I want to make movies of a spatio-temporal evolution of a quantity
> across the cortical surface, not reg/meg.
> > >
> > >
> > > i want to do it at the full resolution of the vertices on the surface,
> so about 300000+ for both hemispheres,there
> > > would be 200-300 time points, so my input would
> > > be a matrix 300000*300.
> > >
> > >
> > > so looking a bit at the manual for men_make_movie ( i have used men
> before for reg solutions and displayed then on the cortical
> > > surface succesfully ). would i use the --stcin option ? I would need
> to know the format for the stc files and skip,
> > > --meas,--inv,--set would i need to fake these operators and input some
> version
> > > of identity matrices ?
> > >
> > >
> > > the threshold and such obvious parameters i remember
> > >
> > >
> > > can ya help me skin this cat ?
> > >
> > >
> > > g
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