[Mne_analysis] make non reg/meg movie
Gregory Kirk
gkirk at wisc.edu
Mon Oct 6 00:05:03 EDT 2014
i think it's assuming i have p values and needs an integer or something ?
mne_make_movie --stcin var.stc --spm --fmin 0.0001 --fmax 0.0045 --fmid 0.001 --view med --mov spm_med.mov
gives fmax must be > fmid
im getting decent movies for my purpose using
mne_make_movie --stcin var.stc --fthresh 100000.0 --fmax 50000000.0 --fmid 5000000.0 --view med --mov med.mov
but have not gotten the scale to be the same as in tksurfer, there i get the low variances, below 0.001 to be dark
with what im using i get shades of red and yellow.
is it doing things at the full vertex resolution or decemating the surface, looks a little pixelated,also is
it doing any spatial smoothing, my data is un smoothed
my data is a variance between [0.0001,0.0045] at each vertex and in any particular timepoint.
cheers
Greg
On 10/05/14, Matti Hamalainen wrote:
>
>
>
>
>
> Greg,
>
> When you use --spm option the --fmin, --fmid, and --fmax values are used directly without any multiplier. Use --fmax instead of --fslope, which is provided for backwards compatibility only. - Matti
>
> On Oct 6, 2014, at 3:04 AM, Eric Larson <larson.eric.d at gmail.com <larson.eric.d at gmail.com>> wrote:
>
>
> > I haven't had to deal with this specific problem -- I would apply trial-and-error with a small number of time samples to converge on the proper scale factor.
> >
> > Eric
> >
> >
> >
> >
> > On Sun, Oct 5, 2014 at 1:15 PM, Gregory Kirk <gkirk at wisc.edu <gkirk at wisc.edu')" target="1">gkirk at wisc.edu> wrote:
> >
> > > solved all of those problems and getting a movie now, but the scale is waaaaay off. seems to me now i remember
> > > mne assumed the data was in pico volts or some other really small numbers, but the actuall data is short or long integers or something
> > > so internally mne applies some huge scaling.
> > >
> > > i rescalled my data from a variance range [0,1] my multiplying by 10,000 thinking that would allow me to use
> > > the integer fmin, fthresh, etc. but now the cortex is solid yellow , i.e. everything abouve the max.
> > >
> > > and the little movie says
> > >
> > > 1.0 .. 50 ..150 * 1e-10
> > >
> > > so what internal scale do i need to account for, i.e. what scale should i apply to data in
> > > a variance range to get this to come out good?
> > >
> > > cheers,
> > >
> > > greg
> > >
> > > On 10/03/14, Eric Larson wrote:
> > > > 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 <https://github.com/mne-tools/mne-python/blob/master/mne/source_estimate.py#L72(javascript:main.compose('new', 't=gkirk at wisc.edu>(java_script:main.compose()> 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'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`:
> > > > > >
> > > > > >
> > > > > > > > > On Thu, Oct 2, 2014 at 2:21 PM, Gregory Kirk <Mne_analysis at nmr.mgh.harvard.edu <Mne_analysis at nmr.mgh.harvard.edu>(java_script:main.compose() <gkirk at wisc.edu <gkirk at wisc.edu>(java_script:main.compose()')" target="1">gkirk at wisc.edu <gkirk at wisc.edu>(java_script:main.compose()> 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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