[Mne_analysis] Index errors with PySurfer real-time source estimate visualization

[Denis-Alexander Engemann]

Hi Sebastian,

before digging deeper,
which version of PySurfer are you using.
In my experience usually many problems dissolve with the latest PySurfer
code.

Best,
Denis


On Tue, Jul 22, 2014 at 1:44 PM, Silfverberg Sebastian <
sebastian.silfverberg at aalto.fi> wrote:

>  Hi everyone!
>
> I have been trying to code a program that would enable to plot trigger
> spesific source estimates in real time with FieldTrip Buffer. I have
> managed to do that, but I want to optimize it a little more. I would like
> the program to be able to plot the initial brain surface with PySurfer and
> then just add and remove estimates from the cortex when the buffer has
> received a next epoch. I'm using PySurfers Brain()-class and brain.add_data
> -method. But the brain.add_data -method doesn't work:
>
> It always complains about index errors. I've noticed that the index error
> happens to be in vertices which have to be given in add_data method. Error
> is for example this:
>
> IndexError                                Traceback (most recent call last)
> /usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in
> execfile(fname, *where)
>     173             else:
>     174                 filename = fname
> --> 175             __builtin__.execfile(filename, *where)
>
> /home/silfves1/mne-python/examples/omatfunktiot/yks_off.py in <module>()
>     122                                  stc.tmin + stc.data.shape[1] *
> stc.tstep,
>     123                                  stc.data.shape[1])
> --> 124 brain.add_data(stc.data, colormap='hot', vertices = stc.vertno,
> smoothing_steps=20, time=time, time_label='Time 100.0 ms', hemi=hemi,
> remove_existing=True)
>
>     125
>     126 # for ii, ev in enumerate(epochs.iter_evoked()):
>
>
> /home/silfves1/.local/lib/python2.7/site-packages/pysurfer-0.5-py2.7.egg/surfer/viz.pyc
> in add_data(self, array, min, max, thresh, colormap, alpha, vertices,
> smoothing_steps, time, time_label, colorbar, hemi,
> remove_existing)
>     835             adj_mat = utils.mesh_edges(self.geo[hemi].faces)
>     836             smooth_mat = utils.smoothing_matrix(vertices, adj_mat,
> --> 837                                                 smoothing_steps)
>     838         else:
>     839             smooth_mat = None
>
> /home/silfves1/.local/lib/python2.7/site-packages/pysurfer-0.5-py2.7.egg/surfer/utils.pyc
> in dec(*args, **kwargs)
>     337             return ret
>     338         else:
> --> 339             return function(*args, **kwargs)
>     340
>     341     # set __wrapped__ attribute so ?? in IPython gets the right
> source
>
>
> /home/silfves1/.local/lib/python2.7/site-packages/pysurfer-0.5-py2.7.egg/surfer/utils.pyc
> in smoothing_matrix(vertices, adj_mat, smoothing_steps,
> verbose)
>
>     512     n_iter = smoothing_steps if smoothing_steps is not None else
> 1000
>     513     for k in range(n_iter):
> --> 514         e_use = e[:, idx_use]
>     515
>     516         data1 = e_use * np.ones(len(idx_use))
>
> /usr/lib/python2.7/dist-packages/scipy/sparse/csr.pyc in __getitem__(self,
> key)
>     218                     return self._get_submatrix(row, col)
> #[1:2,j]
>     219                 else:
> --> 220                     P = extractor(col,self.shape[1]).T
> #[1:2,[1,2]]
>     221                     return self[row,:]*P
>     222
>
> /usr/lib/python2.7/dist-packages/scipy/sparse/csr.pyc in
> extractor(indices, N)
>     186             indices = asindices(indices)
>     187
> --> 188             (min_indx,max_indx) = check_bounds(indices,N)
>     189
>     190             if min_indx < 0:
>
> /usr/lib/python2.7/dist-packages/scipy/sparse/csr.pyc in
> check_bounds(indices, N)
>     172             max_indx = indices.max()
>     173             if max_indx >= N:
> --> 174                 raise IndexError('index (%d) out of range' %
> max_indx)
>     175
>     176             min_indx = indices.min()
>
> IndexError: index (215242) out of range
>
> I don't know how to fix this. Is the stc.vertno same thing as vertices?
> I've also tried to remove some indexes from stc.vertno, but it always
> complains about the ranks not being 1. Do you have any ideas to help me?
>
> Best regards
>
> Sebastian Silfveberg
>
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