[Mne_analysis] make non reg/meg movie

[Gregory Kirk]

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'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'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'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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