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
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
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
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 PhDResearch 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.comThe 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.
-------------- next part --------------
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hi David,
I don't see any mne_setup_source_space
when is your $SUBJECT-5-src.fif generated?
if it were any ico5 it would be named $SUBJECT-ico-5-src.fif
Alex
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
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
fito 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
doneso I am still not sure why I get the ico surface error. BTW I am using mne 2.7.4
thanks //dave
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
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 PhDResearch 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.comThe 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.comThe 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.
-------------- next part --------------
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URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140105/474e05d5/attachment.html
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
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
fito 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
doneso I am still not sure why I get the ico surface error. BTW I am using mne 2.7.4
thanks //dave
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
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 PhDResearch 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:
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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.comThe 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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hi David,
mne_setup_source_space --subject $SUBJECT --overwrite --spacing 5 --cps
-should I be using different parameters: because I get:
use:
mne_setup_source_space --subject $SUBJECT --overwrite --ico 5 --cps
the generated file will be:
$SUBJECT-ico-5-src.fif
Alex
Thanks I appreciate your help
hi David,
mne_setup_source_space --subject $SUBJECT --overwrite --spacing 5 --cps
-should I be using different parameters: because I get:
use:
mne_setup_source_space --subject $SUBJECT --overwrite --ico 5 --cps
the generated file will be:
$SUBJECT-ico-5-src.fif
Alex
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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