[Mne_analysis] setup_soruce_space error

[Eric Larson]

        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>
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
>
>         External Email - Use Caution
>
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