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 :
Please remember to keep the list cced. List please check my response below
for any disagreements which may help Lucille.
Thanks,
D
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,
DHi 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,
DanDear 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 --overwriteSetting 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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