[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 15:50:48 EST 2014
HI Alex,
sorry ... I run the following two steps earler before BEM calculation:
mne_setup_source_space --subject $SUBJECT --overwrite --spacing 5 --cps
-should I be using different parameters: because I get:
files like $SUBJECT-5-src.fif with no ico
On Jan 5, 2014, at 3:08 PM, David I Leitman wrote:
> HI here is what I do:
>
> ########################### Step-4: FORWARD MODEL SETUP ###########################
> echo ++++++++++++++++++++++++++++++++++++Step-4: FORWARD MODEL SETUP
> echo ++++++++++++++++++++++++++++++++++++Step-4: FORWARD MODEL SETUP
> echo ++++++++++++++++++++++++++++++++++++Step-4: FORWARD MODEL SETUP
>
> # ## for meg only model use:
> #mne_setup_forward_model --subject $SUBJECT --surf --ico 4 --homog --overwrite
>
> # ## alternatively use below
> mne_setup_forward_model --subject $SUBJECT --surf --ico 4 --overwrite
>
> # ## create bem 3 shell models for eeg as well as model for meg
> # ## sometimes misalignment of surfaces can give the following error:
> # ## "Checking that inner skull surface is inside outer skull surface...[failed]
> # ## Surface inner skull is not completely inside surface outer skull(sum of solid angles = 1.8995e-16 * 4*PI).
> # ## Could't create the geometry file"
> # ## in such a case att eh following
> if [ $? == 1 ]; then
> mne_setup_forward_model --subject $SUBJECT --surf --ico 4 --overwrite --outershift 2.0
> if [ $? == 1 ]; then
> mne_setup_forward_model --subject $SUBJECT --surf --ico 4 --overwrite --outershift 2.0 --innershift 1.0
> fi
> fi
>
>
> to do the forward solution I do:
>
>
> for file in $SUBJECTS_DIR/$SUBJECT/meg/${SUBJECT}_AR-epoched.fif;
> do
> echo $file
> echo +++++++++++++++++++++++ doing Forward solution epoched fiffile
> echo +++++++++++++++++++++++ doing Forward solution epoched fiffile
> echo +++++++++++++++++++++++ doing Forward solutionepoched fiffile
>
> # for MEG only
> mne_do_forward_solution \
> --subject $SUBJECT \
> --src $SUBJECT-5-src.fif \
> --bem $SUBJECT-5120-5120-5120-bem-sol.fif \
> --meas $file \
> --megonly \
> --fwd ${SUBJECT}_AR-epoched-${SUBJECT}-5-meg-src-fwd.fif \
> --overwrite
>
> # for EEG only
> mne_do_forward_solution \
> --subject $SUBJECT \
> --src $SUBJECT-5-src.fif \
> --bem $SUBJECT-5120-5120-5120-bem-sol.fif \
> --meas $file \
> --eegonly \
> --fwd ${SUBJECT}_AR-epoched-${SUBJECT}-5-eeg-src-fwd.fif \
> --overwrite
>
> # for EEG & MEEG only
> mne_do_forward_solution \
> --subject $SUBJECT \
> --src $SUBJECT-5-src.fif \
> --bem $SUBJECT-5120-5120-5120-bem-sol.fif \
> --meas $file \
> --fwd ${SUBJECT}_AR-epoched-${SUBJECT}-5-meg_eeg-src-fwd.fif \
> --overwrite
> done
>
>
> so I am still not sure why I get the ico surface error. BTW I am using mne 2.7.4
>
> thanks //dave
> On Jan 5, 2014, at 2:31 PM, Alexandre Gramfort wrote:
>
>> hi David,
>>
>> how do you generate your source spaces? To use this tool, you should
>> use the -ico option.
>>
>> Something like:
>>
>> mne_setup_source_space --oct 6 --subject sample
>>
>> for an oct 6 source space with approx 8000 locations or
>>
>> mne_setup_source_space --ico 5 --subject sample
>>
>> for an ico 5 source space with approx 20000 locations.
>>
>> If you have an old MNE version use:
>>
>> mne_setup_source_space --ico -6 --subject sample
>>
>> for the oct 6.
>>
>> Hope this helps,
>>
>> Alex
>>
>>
>>
>> On Sun, Jan 5, 2014 at 2:02 PM, David I Leitman
>> <leitman at mail.med.upenn.edu> wrote:
>>> 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
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>>> 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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>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
> 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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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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