# problem with mne\_setup\_source\_space : Source space	creation failed

**URL:** <https://mne.discourse.group/t/problem-with-mne-setup-source-space-source-space-creation-failed/582>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [May 21, 2013, 2:00pm UTC](https://mne.discourse.group/t/problem-with-mne-setup-source-space-source-space-creation-failed/582 "2013-05-21T14:00:04Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [May 21, 2013, 2:00pm UTC](https://mne.discourse.group/t/problem-with-mne-setup-source-space-source-space-creation-failed/582/1 "2013-05-21T14:00:04Z")

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Dear All,

I have a problem with the creation of the source space  
(mne\_setup\_source\_space) with the -ico 5 option for one particular  
subject. Here is the error reported by MNE :

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [May 23, 2013, 2:24pm UTC](https://mne.discourse.group/t/problem-with-mne-setup-source-space-source-space-creation-failed/582/2 "2013-05-23T14:24:21Z")

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Please remember to keep the list cced. List please check my response below  
for any disagreements which may help Lucille.

Thanks,  
D

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [May 23, 2013, 5:02pm UTC](https://mne.discourse.group/t/problem-with-mne-setup-source-space-source-space-creation-failed/582/3 "2013-05-23T17:02:07Z")

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2013/5/23 Lucille Lecoutre \<lu.lecoutre at gmail.com\>

> Hi Dan,
> 
> I am not totally sure if this is a problem or not for the group analyses,  
> as I this is the first time I do source reconstruction with MEG. The only  
> thing I could think about is that it could introduce a statistical bias in  
> the grand averaging procedure given the different number of vertices.  
> Here is my procedure after having computed the inverse model : I make a  
> grand average of my source estimates (using mne\_average\_estimates), and  
> then selecting visual and auditory labels on the fsaverage brain. All the  
> subsequent analysis are done within these labels.  
> I haven't tried to go through the whole procedure with this particular  
> subject porcessed with ico -6 so far. I should probably check first that  
> mne\_average\_estimates accepts to average source estimates (produced with  
> mne\_python) having a different number of vertices.
> 
> Thank you very much for your help,
> 
> Lucille
> 
> 2013/5/23 dgw \<dgwakeman at gmail.com\>
> 
> > Hi Lucille,
> > 
> > While it might be the preferable option, I cannot see a reason why it  
> > should be necessary unless you are comparing different groups (like one  
> > group with several participants with this issue and another that doesn't  
> > have any like this). Assuming you do the morphing and smoothing  
> > appropriately for this participant and for the others (that is more  
> > smoothing according to the source space decimation), I would not have a  
> > problem with this as a reviewer (though perhaps other readers may disagree:  
> > please speak up if you can see a problem). It shouldn't introduce any error  
> > (assuming the rest of your analysis is appropriate i.e. appropriate  
> > looseness type orientation constraint etc.).
> > 
> > Although, I guess given the automated nature, it is likely fairly simple  
> > to re-generate your source space, forward model and inverse solutions for  
> > this data (depending on how complex your analysis is).
> > 
> > HTH,  
> > D
> > 
> > > Hi Dan,
> > > 
> > > Thank you very much for your reply.  
> > > I guess I will then have to redo the analyses for each subject with the  
> > > -6 option if I want to include this one in the group analysis...
> > > 
> > > Lucille
> > > 
> > > 2013/5/23 dgw \<dgwakeman at gmail.com\>
> > > 
> > > > Hi Lucille,
> > > > 
> > > > This is due to the nature of this participant's source space.  
> > > > Unfortunately, the only remedies are to use a different ico setting (with a  
> > > > lower number of vertices, for example -6) or to use the -spacing option).
> > > > 
> > > > HTH,  
> > > > Dan
> > > > 
> > > > > Dear All,
> > > > > 
> > > > > I have a problem with the creation of the source space  
> > > > > (mne\_setup\_source\_space) with the -ico 5 option for one particular  
> > > > > subject. Here is the error reported by MNE :
> > > > > 
> > > > > --------------------------------------------------------------  
> > > > > $ mne\_setup\_source\_space --ico 5 --overwrite
> > > > > 
> > > > > Setting up the source space with the following parameters:
> > > > > 
> > > > > SUBJECTS\_DIR = /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri/  
> > > > > Subject = tc\_120199  
> > > > > Surface = white  
> > > > > Icosahedron subdivision grade 5
> > > > > 
> > > > > \>\>\> 1. Creating the source space file  
> > > > > /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri//tc\_120199/bem/tc\_120199-ico-5-src.fif...
> > > > > 
> > > > > mne\_make\_source\_space version 2.6 compiled at May 6 2013 04:18:39
> > > > > 
> > > > > Loading  
> > > > > /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri//tc\_120199/surf/lh.white...  
> > > > > Triangle file : created by LLECOUTR on Wed May 1 02:26:12 2013 nvert  
> > > > > = 136783 ntri = 273562  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Triangle and vertex normals and neighboring triangles...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Vertex neighbors...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Distances between neighboring vertices...[820686 distances done]  
> > > > > Doing the icosahedral vertex picking...  
> > > > > Loading geometry from  
> > > > > /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri//tc\_120199/surf/lh.sphere...  
> > > > > Triangle file : created by LLECOUTR on Wed May 1 03:29:58 2013 nvert  
> > > > > = 136783 ntri = 273562  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Triangle and vertex normals and neighboring triangles...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Vertex neighbors...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Distances between neighboring vertices...[61440 distances done]  
> > > > > Mapping lh tc\_120199 -\> ico (5) ...[done]  
> > > > > Setting up the triangulation for the decimated surface...  
> > > > > loaded lh.white 10242/136783 selected to source space (ico = 5)
> > > > > 
> > > > > Loading  
> > > > > /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri//tc\_120199/surf/rh.white...  
> > > > > Triangle file : created by LLECOUTR on Wed May 1 04:55:58 2013 nvert  
> > > > > = 137309 ntri = 274614  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Triangle and vertex normals and neighboring triangles...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Vertex neighbors...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Distances between neighboring vertices...[823842 distances done]  
> > > > > Doing the icosahedral vertex picking...  
> > > > > Loading geometry from  
> > > > > /neurospin/meg/meg\_tmp/AVclock\_Lucille\_2013/mri//tc\_120199/surf/rh.sphere...  
> > > > > Triangle file : created by LLECOUTR on Wed May 1 06:15:31 2013 nvert  
> > > > > = 137309 ntri = 274614  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Triangle and vertex normals and neighboring triangles...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Vertex neighbors...[done]  
> > > > > &nbsp;&nbsp;&nbsp;&nbsp;Distances between neighboring vertices...[61440 distances done]  
> > > > > Mapping rh tc\_120199 -\> ico (5) ...[done]  
> > > > > Source space vertex moved from 57859 to 55128 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 57859 to 52619 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 55128 to 52611 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 52619 to 57845 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 57845 to 57835 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 57835 to 57846 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 57860 to 59133 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 59133 to 60383 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 60383 to 59154 because of double  
> > > > > occupation.  
> > > > > Source space vertex moved from 52619 to 53812 because of double  
> > > > > occupation.  
> > > > > vertex 57859 is in the map multiple times.  
> > > > > Cannot continue  
> > > > > Source space creation failed  
> > > > > Temporary files removed.  
> > > > > ---------------------------------------------
> > > > > 
> > > > > I saw that this problem has been reported before (see this thread\<[https://mail.nmr.mgh.harvard.edu/pipermail//mne\_analysis/2011-November/000837.html&gt;from](https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2011-November/000837.html&gt;from) November 2011).  
> > > > > I tried as suggested by Alex to use the -ico -6 option and it works  
> > > > > perfectlly well.The problem with that solution is that I want to work with  
> > > > > the FreeSurfer average brain, all the other subjects have been processed  
> > > > > with the ico 5 option.
> > > > > 
> > > > > So here are my questions :  
> > > > > Does it make sense at all to work on an fsaverage brain if the number  
> > > > > of the sources are not the same across subjects?  
> > > > > It is said in the previous thread that this a known problem, and that  
> > > > > it is caused by "some safety checks run by MNE". Is there any way to bypass  
> > > > > these sanity checks?
> > > > > 
> > > > > Many thanks,
> > > > > 
> > > > > Lucille Lecoutre
> > > > > 
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