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<p>Hi Eric,</p>
<p><br>
</p>
<p> Thanks for your response. Do you get the "double occupation" error as well?</p>
<p><br>
</p>
<p> It is possible that this is all an error on my part. Has anyone out there successfully used --morph with mne_setup_source_space in the past several years?</p>
<p><br>
</p>
<p> I get the same thing at the 2.7.0 level of the code as well. I would be open to using a downlevel release, such as that where this functionality was originally introduced. At the moment 2.7.0 appears to be the oldest code still available.</p>
<p><br>
</p>
<p> Thanks again,</p>
<p><br>
</p>
<p>-Per</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size: 11pt;"><b>From:</b> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Eric Larson <larson.eric.d@gmail.com><br>
<b>Sent:</b> Friday, January 30, 2015 11:25 AM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] mne_setup_source_space with --morph: double occupation error</font>
<div> </div>
</div>
<div>
<div dir="ltr">I don't have much experience with the --morph option. But I can also confirm that I could not get the --morph option to work just now, despite trying a number of different source and destination subjects, and spacing options, even on the latest
nightly.
<div><br>
</div>
<div>When porting the setup_source_space code to python, we omitted the --morph option for two reasons: 1) the additional coding complexity implementing it required, and 2) uncertainty about how often it was actually used. If you're feeling brave, we can help
you implement it :) Either way, feel free to open an issue on the mne-python Github page requesting the feature. You might be able to nerd snipe developer with it, especially if other people show interest.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Eric</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div><br>
</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Jan 30, 2015 at 9:54 AM, Per Arnold Lysne <span dir="ltr">
<<a href="mailto:lysne@unm.edu" target="_blank">lysne@unm.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;">
Hi Martin and Jon,<br>
<br>
Thanks for your replies:<br>
<br>
Martin: Unfortunately I am having the same problem with the nightly build<br>
<br>
Jon: I think I have asked you about something similar in the past and I was already working from a copy of this document. I have tried morphing to another subject in the experiment, as opposed to fsaverage, but encountered the same problem. At your suggestion
I used Freesurfer "make_average_subject" two create an average brain from other subjects in the experiment (ok, two subjects, including the one being morphed), but - same problem.<br>
<br>
I had thought I might try the Python option mne.setup_source_space, but it does not appear to support a morphing option.<br>
<br>
Are there any other ideas out there? Thanks for everyone's help,<br>
<br>
-Per<br>
<br>
________________________________________<br>
From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> on behalf of Martin Luessi <<a href="mailto:mluessi@nmr.mgh.harvard.edu">mluessi@nmr.mgh.harvard.edu</a>><br>
Sent: Thursday, January 29, 2015 11:24 AM<br>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu">mne_analysis@nmr.mgh.harvard.edu</a><br>
Subject: Re: [Mne_analysis] mne_setup_source_space with --morph: double occupation error<br>
<div class="HOEnZb">
<div class="h5"><br>
Hi Per,<br>
<br>
You could also try using the nightly version of MNE. If I remember<br>
correctly, this error happens due to numerical precision and we changed<br>
so things to use double precision to prevent it.<br>
<br>
Best,<br>
<br>
Martin<br>
<br>
<br>
On 01/29/15 13:19, Jon Houck wrote:<br>
> Hi Per,<br>
><br>
> If the inversion would happen in the common space, rather than morphing<br>
> the source space you might try the pipeline Matti posted awhile ago for<br>
> using fsaverage as a surrogate (attached). You could use some other<br>
> brain as the template (say, an average brain created from your sample).<br>
> This is obviously a bit of a kludge, but would help you to avoid this<br>
> specific error (while also causing other less obvious problems).<br>
><br>
> Jon<br>
><br>
><br>
><br>
> On Wed, Jan 28, 2015 at 3:56 PM, Per Arnold Lysne <<a href="mailto:lysne@unm.edu">lysne@unm.edu</a><br>
> <mailto:<a href="mailto:lysne@unm.edu">lysne@unm.edu</a>>> wrote:<br>
><br>
> Hello All,<br>
><br>
><br>
> My apologies for posting about an issue which has already<br>
> received considerable coverage. I am trying to use<br>
> mne_setup_source_space with the --morph option. I am doing this<br>
> because I am working on an analysis which requires all subjects to<br>
> be in a common vertex space early on (so mne_make_movie is too late).<br>
><br>
><br>
> For example:<br>
><br>
><br>
> mne_setup_source_space --subject <subject_id> --morph fsaverage<br>
><br>
><br>
> I am receiving the "double occupation" error which is mentioned<br>
> numerous times in this forum:<br>
><br>
><br>
> Source space vertex moved from 158588 to 112571 because of double<br>
> occupation.<br>
> Source space vertex moved from 39211 to 158591 because of double<br>
> occupation.<br>
> Source space vertex moved from 158587 to 126593 because of double<br>
> occupation.<br>
> Source space vertex moved from 126593 to 126594 because of double<br>
> occupation.<br>
> Source space vertex moved from 126593 to 126592 because of double<br>
> occupation.<br>
> Source space vertex moved from 126594 to 126595 because of double<br>
> occupation.<br>
> Source space vertex moved from 158590 to 87784 because of double<br>
> occupation.<br>
> Source space vertex moved from 87782 to 112573 because of double<br>
> occupation.<br>
> vertex 27923 would be used multiple times.<br>
> Source space creation failed<br>
> Temporary files removed.<br>
><br>
><br>
> My understanding from the previous posts is that this error can<br>
> be avoided by either using --spacing with any distance given, or<br>
> with --ico and a relatively small number of vertices (according to<br>
> table 3.1 of the 2.7.3 manual, this means smaller absolute integer<br>
> values, such as --ico 3 or --ico -4). Unfortunately I am still<br>
> getting this error regardless of what I give to --spacing (1-21 have<br>
> been tried) or with both larger and smaller values for --ico (1-7<br>
> both positive and negative).<br>
><br>
><br>
> This problem does not appear to be limited to any particular<br>
> subject in my analysis, nor to the fsaverage brain. I am working<br>
> under Ubuntu 13.10, and my version of mne_make_source_space is as<br>
> follows:<br>
><br>
><br>
> mne_make_source_space version 2.5 compiled at Jan 6 2011 02:25:18<br>
><br>
><br>
> Am I understanding the previous posts correctly? Is there any<br>
> new progress on this issue? Are there other ways to avoid it? (I see<br>
> there is a setup_source_space in the Python code - should I try that?)<br>
><br>
><br>
> Thanks again,<br>
><br>
><br>
> Per Lysne<br>
><br>
> University of New Mexico<br>
><br>
><br>
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<br>
--<br>
Martin Luessi, Ph.D.<br>
<br>
Research Fellow<br>
<br>
Department of Radiology<br>
Athinoula A. Martinos Center for Biomedical Imaging<br>
Massachusetts General Hospital<br>
Harvard Medical School<br>
149 13th Street<br>
Charlestown, MA 02129<br>
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