[Mne_analysis] setup_soruce_space error

[Bear, Joshua]

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




> On Mar 5, 2019, at 2:47 PM, Eric Larson <larson.eric.d at gmail.com> wrote:
> 
>         External Email - Use Caution        
> 
> 
> 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
> 
> 
> On Tue, Mar 5, 2019 at 4:07 PM Bear, Joshua <JOSHUA.BEAR at ucdenver.edu <mailto:JOSHUA.BEAR at ucdenver.edu>> wrote:
> 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:
> 
> SUBJECTS_DIR = /Users/joshbear/clinical/meg/anat/
> Subject      = E-0192
> Surface      = white
> Icosahedron subdivision grade 5
> 
> >>> 1. Creating the source space...
> 
> 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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