[Mne_analysis] plot_label_from_stc.py: Exception: The source space does not appear to be an ico surface

Sun Jan 5 08:06:48 EST 2014

Hi all

I have been trying to run portions of the code contained in the example "plot_label_from_stc.py" going through line by line thing are well until this command:

func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=5,
                                 subjects_dir=subjects_dir, connected=True)

at this point i get the following output errors:

Reading labels from parcellation..
Triangle file: created by neuromag on Wed Feb 20 19:45:05 2013 nvert = 136162 ntri = 272320
  read 34 labels from /mnt/thothdisk1/K_AWARD/K_DATA/MEG_DATA/L7689/label/lh.aparc.annot
Triangle file: created by neuromag on Wed Feb 20 22:57:01 2013 nvert = 138400 ntri = 276796
  read 34 labels from /mnt/thothdisk1/K_AWARD/K_DATA/MEG_DATA/L7689/label/rh.aparc.annot
[done]
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-223-de7294e7cf08> in <module>()
     6 
     7 func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=5,
----> 8                                   subjects_dir=subjects_dir, connected=True)
     9 

/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/label.pyc in stc_to_label(stc, src, smooth, connected, subjects_dir)
   642         rr = [1e3 * src[0]['rr'], 1e3 * src[1]['rr']]
   643         tris = [src[0]['tris'], src[1]['tris']]
--> 644         src_conn = spatial_src_connectivity(src).tocsr()
   645 
   646     labels = []

/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/utils.pyc in dec(*args, **kwargs)
   378             return ret
   379         else:
--> 380             return function(*args, **kwargs)
   381 
   382     # set __wrapped__ attribute so ?? in IPython gets the right source

/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/source_estimate.pyc in spatial_src_connectivity(src, dist, verbose)
  2216         The connectivity matrix describing the spatial graph structure.
  2217     """
-> 2218     return spatio_temporal_src_connectivity(src, 1, dist)
  2219 
  2220 

/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/utils.pyc in dec(*args, **kwargs)
   378             return ret
   379         else:
--> 380             return function(*args, **kwargs)
   381 
   382     # set __wrapped__ attribute so ?? in IPython gets the right source

/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/source_estimate.pyc in spatio_temporal_src_connectivity(src, n_times, dist, verbose)
  2072     if dist is None:
  2073         if src[0]['use_tris'] is None:
-> 2074             raise Exception("The source space does not appear to be an ico "
  2075                             "surface. Connectivity cannot be extracted from "
  2076                             "non-ico source spaces.")

Exception: The source space does not appear to be an ico surface. Connectivity cannot be extracted from non-ico source spaces.

Do you have any suggestions when query 
inverse_operator['src']
Out[227]: <SourceSpaces: [<'surf', n_vertices=136162, n_used=5759>, <'surf', n_vertices=138400, n_used=5838>]>

so I think the space should be an ico surface

thanks //dave
David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page:	http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
 http://davidileitman.com

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above.  If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited.  If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.

David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page:	http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
 http://davidileitman.com

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above.  If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited.  If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.

David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page:	http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
 http://davidileitman.com

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above.  If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited.  If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.

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