# problem with setting up the source space **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [May 22, 2017, 6:51pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223 "2017-05-22T18:51:43Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 22, 2017, 6:51pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223/1 "2017-05-22T18:51:43Z")
Hi all, I got the following error when creating the source space with mne.setup\_source\_space(). The spacing was set to 'ico5'. \*Triangle file: created by lw604 on Sat Dec 3 16:57:00 2016 nvert = 145568 ntri = 291132\* \*Mapping lh 08\_NonCon -\> ico (5) ...\* \* Source space vertex moved from 145214 to 145216 because of double occupation\* \* Source space vertex moved from 56257 to 56268 because of double occupation\* \* Source space vertex moved from 56268 to 145227 because of double occupation\* \* Source space vertex moved from 145227 to 57616 because of double occupation\* \*Traceback (most recent call last):\* \* File "\", line 3, in \\* \* File "\", line 2, in setup\_source\_space\* \* File "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/utils.py", line 708, in verbose\* \* return function(\*args, \*\*kwargs)\* \* File "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/source\_space.py", line 1311, in setup\_source\_space\* \* subjects\_dir)\* \* File "/autofs/cluster/kuperberg/nonconMM/MEG/python/anaconda/lib/python2.7/site-packages/mne/surface.py", line 677, in \_create\_surf\_spacing\* \* '%d / %d' % (k, nmap))\* \*RuntimeError: Could not find neighbor for vertex 8590 / 10242\* I have completed the cortical surface reconstruction with FreeSurfer. Also, there was no error when I set spacing = 'oct6'. We have 32 participants, and only two participants have this type of error. What should I do? Thanks for your help! Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20170522/8f05d94a/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170522/8f05d94a/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 22, 2017, 6:57pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223/2 "2017-05-22T18:57:16Z")
In lieu of a better (code) fix, I'd use the default oct6 spacing. Is there a reason you prefer ico5? Do these subjects have particularly small heads by any chance? Eric ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 22, 2017, 7:22pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223/3 "2017-05-22T19:22:28Z")
Hi Eric, Thanks for your quick response! I used ico5 to have a better spatial resolution. I saw several other papers used this setting. I quickly checked five participants. Indeed it seems that these two subjects have smaller brain than others. But I still don't understand why the higher resolution causes this error. I thought the smaller spacing should result in more neighbors... Thanks again for your help! Lin ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 22, 2017, 7:35pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223/4 "2017-05-22T19:35:21Z")
> I used ico5 to have a better spatial resolution. I saw several other > papers used this setting. I wouldn't expect it to give much better spatial resolution in practice, at least for distributed solvers. (Not sure about sparse ones, but I doubt it.) But I still don't understand why the higher resolution causes this error. I > thought the smaller spacing should result in more neighbors... The "neighbors" here aren't probably aren't quite what you're thinking of, which sound like neighbors in the \*low-resolution\* mesh that results from setting up the source space. IIRC the source space is constructed by downsampling the high-resolution FreeSurfer mesh, specifically by recursively subdividing a standard icosahedron (ico) or octahedron (oct), doing a nearest-neighbor mapping to the subject's high-resolution sphere surface, and then de-duplicating any vertices that are nearest neighbors to more than one of the ico/oct vertices. The de-duplication thus uses the neighbors according to the high-resolution mesh triangulation. This error suggests that there are no neighbors left to choose from, i.e. they are all already in the source space, and thus the deduplication process could not succeed. In theory we might be able to work around this in the code by e.g. removing any vertices (or really equating them in their mesh with their best duplicate) that happen to have this problem. This might lead lead to some unintended consequences, though, such as a less uniform sampling of the surfaces, so it would need some thought, work, and testing to get right. Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20170522/57fdd6ff/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170522/57fdd6ff/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 22, 2017, 9:23pm UTC](https://mne.discourse.group/t/problem-with-setting-up-the-source-space/1223/5 "2017-05-22T21:23:49Z")
Thanks so much, Eric! It makes sense to me now. I'll take your suggestion to use the 'oct6'. 🙂 Best, Lin