I received an error message when using setup_source_space with spacing=?ico5?. It states that it could not find a neighbor for vertex 8015 / 10242. The Freesurfer segmentation looks pretty good, and when I use setup_source_space with spacing=?oct6? it works fine. I?ve also used this same script (and, ergo, the same source space call) with several other subjects without error. Any thoughts on the best way to resolve this? Error code below.
Doing the icosahedral vertex picking...
Loading /Users/joshbear/clinical/meg/anat/E-0192/surf/lh.white...
Mapping lh E-0192 -> ico (5) ...
Triangle neighbors and vertex normals...
Loading geometry from /Users/joshbear/clinical/meg/anat/E-0192/surf/lh.sphere...
Source space vertex moved from 154860 to 154932 because of double occupation
Source space vertex moved from 154862 to 154866 because of double occupation
Source space vertex moved from 154908 to 154891 because of double occupation
Source space vertex moved from 154866 to 154868 because of double occupation
Source space vertex moved from 154932 to 154938 because of double occupation
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<string>", line 2, in setup_source_space
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 952, in verbose
return function(*args, **kwargs)
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/source_space.py", line 1470, in setup_source_space
subjects_dir)
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/surface.py", line 732, in _create_surf_spacing
'%d / %d' % (k, nmap))
RuntimeError: Could not find neighbor for vertex 8015 / 10242
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Is the brain in question small? If so it might be too small to work with
ico-5 spacing (which has 10242 verts as opposed to oct-6's 4098). You could
switch to using oct-6 for all your subjects.
I think I switched to ico5 because I ran into some problem morphing to fsaverage so that I could use the HCPMMP labels with oct6. I?ll give it a try, though, as I don?t recall what the specific problem was ? to be continued!
Thank you,
Josh
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Is the brain in question small? If so it might be too small to work with ico-5 spacing (which has 10242 verts as opposed to oct-6's 4098). You could switch to using oct-6 for all your subjects.
Eric
Hi all,
I received an error message when using setup_source_space with spacing=?ico5?. It states that it could not find a neighbor for vertex 8015 / 10242. The Freesurfer segmentation looks pretty good, and when I use setup_source_space with spacing=?oct6? it works fine. I?ve also used this same script (and, ergo, the same source space call) with several other subjects without error. Any thoughts on the best way to resolve this? Error code below.
Thank you,
Josh
>>> src = mne.setup_source_space(subject, spacing='ico5', subjects_dir=mri_root_directory)
Setting up the source space with the following parameters:
Doing the icosahedral vertex picking...
Loading /Users/joshbear/clinical/meg/anat/E-0192/surf/lh.white...
Mapping lh E-0192 -> ico (5) ...
Triangle neighbors and vertex normals...
Loading geometry from /Users/joshbear/clinical/meg/anat/E-0192/surf/lh.sphere...
Source space vertex moved from 154860 to 154932 because of double occupation
Source space vertex moved from 154862 to 154866 because of double occupation
Source space vertex moved from 154908 to 154891 because of double occupation
Source space vertex moved from 154866 to 154868 because of double occupation
Source space vertex moved from 154932 to 154938 because of double occupation
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<string>", line 2, in setup_source_space
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 952, in verbose
return function(*args, **kwargs)
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/source_space.py", line 1470, in setup_source_space
subjects_dir)
File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/surface.py", line 732, in _create_surf_spacing
'%d / %d' % (k, nmap))
RuntimeError: Could not find neighbor for vertex 8015 / 10242
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