[Mne_analysis] regarding morphing in matlab

Pavan Ramkumar pavan at neuro.hut.fi
Mon Mar 14 07:00:17 EDT 2011
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Dear MNE users,

Just a follow up mail to my previous request. I would like to transform my
data from one decimated source space to another from within matlab. Below
are the steps I have adopted to do so. If anybody has previous experience
in doing similar things, kindly share your thoughts.

1/ I precomputed the morph maps from each surface to the common brain with
mne_make_morph_maps.

2/ I read in the morph maps using mne_read_morph_maps as follows:
[leftmap,rightmap] = mne_read_morph_map('my_brain', 'common_brain');

3/ I read in an inverse operator for the input surface 'my_brain' into the
structure 'inv_op'

4/ I read in a sample stc file for the target surface i.e. 'common_brain'
to get the vertex info. The stc files were read into 'stc_l' and 'stc_r'

5/ Next, I used the following lines of code to transform my data:
leftmapRelevant = leftmap(stc_l.vertices,inv_op.src(1).vertno);
rightmapRelevant = rightmap(stc_r.vertices,inv_op.src(2).vertno);
morphed_dataL = leftmapRelevant*dataL;
morphed_dataR = rightmapRelevant*dataR;

Note that stc_l.vertices contains all used vertices for the left
hemishpere of the target surface (i.e. 'common_brain') and
inv_op.src(1).vertno contains all used vertices for the left hemisphere of
the source surface (i.e. 'my_brain'). The same is true for stc_r.vertices
and inv_op.src(2).vertno respectively.

Intuition suggests that these steps would suffice, but I did some checks
and figured that most rows of leftmapRelevant and rightmapRelevant are
entirely zero.

I am using a morphgrade of 4 i.e. target surface consists of 2562 used
vertices per hemisphere. By comparison, the source surfaces are computed
with 5mm spacing and therefore consist of about 5000 used vertices per
hemisphere.

What am I missing?

Thank you for your time.
Best regards,
Pavan

> Dear MNE users,
>
> I would like to morph my data from a single subject into a common brain.
> However, instead of writing the result out as an stc file (which takes up
> too much space) I would like to do the morphing from within matlab, and
> then subsequently do some postprocessing on the morphed data before I
> write out stc files.
>
> Does anybody know where to find the vertex numbers corresponding to the
> --morphgrade parameter used in mne_make_movie? Specifically, for
> morphgrade = 5, where do I find the indices of the 10242 vertices that are
> selectively stored into the stc file by mne_make_movie? As far as I
> looked, the manual does not explicitly give this information.
>
> Please advice.
>
> Thanks in advance,
> Pavan
>




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