[Mne_analysis] plot_label_from_stc.py: Exception: The source space does not appear to be an ico surface
David I Leitman
leitman at mail.med.upenn.edu
Sun Jan 5 08:09:19 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.
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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