search

mne-tools / mne-python

MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
https://mne.tools
BSD 3-Clause "New" or "Revised" License
2.62k stars 1.3k forks source link

the 'spatial_exclude' parameter of the function 'spatial_temporal_clustering' #3850

Closed dongqunxi closed 7 years ago

dongqunxi commented 7 years ago

Dear all,

I want to get the significant clusters on the cortices, the function spatial_temporal_clustering estimates the vertices on the surface of the whole brain. I do not want to take the medial central vertices into account. since they do not include any known cortical regions. In my understanding of the parameter 'spatial_exclude', it can exclude the vertices of this region.

My question is that if it makes sense, how do we get the indices of these vertices to be excluded?

Thanks a lot!

larsoner commented 7 years ago

There are lh.Medial_wall.label and rh.Medial_wall.label in fsaverage/label that comes with FreeSurfer, though see also

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031908.html

dongqunxi commented 7 years ago

Thanks a lot, Eric. One additional question, some of the indices from lh.Medial and rh.Medial regions are the same, if I set the parameter 'spatial_exclude', how to organize the list of indices for excluding?

Best wishes, Qunxi Dong

2016-12-16 22:40 GMT+08:00 Eric Larson notifications@github.com:

Closed #3850 https://github.com/mne-tools/mne-python/issues/3850.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/3850#event-896767729, or mute the thread https://github.com/notifications/unsubscribe-auth/ADqbM_WhV7vCUmn-FowRH3KQLLdd_f_Pks5rIqLegaJpZM4LN-yh .

larsoner commented 7 years ago

Are you using the standard fsaverage surface (ico-5)? If so then you need to add 10242 to the right-hemisphere vertex numbers.

If you are using a different subject or different surface, it's more complicated because you have to deal with indexing indices.

dongqunxi commented 7 years ago

Thanks a lot for your help, I am using (ico-5). :-)

Best wishes, Qunxi Dong

2016-12-17 2:27 GMT+08:00 Eric Larson notifications@github.com:

Are you using the standard fsaverage surface (ico-5)? If so then you need to add 10242 to the right-hemisphere vertex numbers.

If you are using a different subject or different surface, it's more complicated because you have to deal with indexing indices.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/3850#issuecomment-267662448, or mute the thread https://github.com/notifications/unsubscribe-auth/ADqbM8KQTlnGzjR_W0jMZq8TNbGv53s9ks5rItgSgaJpZM4LN-yh .