[Mne_analysis] Fwd: problem with mne_setup_source_space : Source space creation failed

Thu May 23 10:24:21 EDT 2013

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

Thanks,
D

---------- Forwarded message ----------
From: dgw <dgwakeman at gmail.com>
Date: Thu, May 23, 2013 at 10:21 AM
Subject: Re: [Mne_analysis] problem with mne_setup_source_space : Source
space creation failed
To: Lucille Lecoutre <lu.lecoutre 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

On Thu, May 23, 2013 at 9:54 AM, Lucille Lecoutre <lu.lecoutre at gmail.com>wrote:

> 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
>>
>>
>> On Tue, May 21, 2013 at 10:00 AM, Lucille Lecoutre <lu.lecoutre at gmail.com
>> > wrote:
>>
>>> 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
>>>     Triangle and vertex normals and neighboring triangles...[done]
>>>     Vertex neighbors...[done]
>>>     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
>>>     Triangle and vertex normals and neighboring triangles...[done]
>>>     Vertex neighbors...[done]
>>>     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
>>>     Triangle and vertex normals and neighboring triangles...[done]
>>>     Vertex neighbors...[done]
>>>     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
>>>     Triangle and vertex normals and neighboring triangles...[done]
>>>     Vertex neighbors...[done]
>>>     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>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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