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<DIV>Hi Ricardo,</DIV>
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<DIV>I have two hints that might help. Firstly, the segmentations and the corresponding meshes can not only intersect each other, but it can also happen that the generated meshes are self-intersecting. This can not be seen from the plots of the segmented brain. The probability for intersections is higher, in my experience, with finer mesh resolutions. You could try something like [800 800 600] instead of [3000 2000 1000]. I usually do some trial and error and then check the volumes with om_check_vol(vol), which will report any intersections and self-intersections in the meshes. The openmeeg plugin needs to be installed for that. </DIV>
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<DIV>Secondly, for to the '\tmp\xyz...': Some of the methods for generating headmodels (at least I know for dipoli and openmeeg) write large temporary files to the hard disk. They have a long random name in order to avoid that some other data is overwritten. These files might get very large, some GB, and they are written per default to \tmp. A while ago I had the problem the temporary files got larger than the space that our system administrator allowed for \tmp. The script ran without errors, but the mat in the resulting structure was empty. The solution was to change the file destination folder to something other than \tmp, which needs to be done directly within the code of the called function (there is no cfg-option or so for that).</DIV>
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<DIV>Hope that helps,</DIV>
<DIV>Gregor <BR><BR></DIV>
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<DIV>-- <BR>Dr. rer. nat. Gregor Volberg <<A href="mailto:gregor.volberg@psychologie.uni-regensburg.de">gregor.volberg@psychologie.uni-regensburg.de</A>> ( <A href="mailto:gregor.volberg@psychologie.uni-regensburg.de">mailto:gregor.volberg@psychologie.uni-regensburg.de</A> )<BR>University of Regensburg<BR>Institute for Experimental Psychology<BR>93040 Regensburg, Germany<BR>Tel: +49 941 943 3862 <BR>Fax: +49 941 943 3233<BR><A href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html</A><BR>>>> Ricardo Moura <ricardoojm@gmail.com> 28.03.2013 18:39 >>><BR></DIV>
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<DIV>Hi Jörn, <BR>thank you very much for your response!<BR></DIV>I checked the segmentation and everything seems to be ok (as far as I can say... No error messages were shown during the processing and I checked the generated objects and plots).<BR><BR></DIV>But I had a strange error while preparing the head model. Somehow the command cannot find the dipoli files, even thought they are really where they should be. And the second message ("/tmp/tp2619f3f3_574d_478a_bfbb_01193b4f8e0c.ama'") I really have no clue of what it means.<BR><BR></DIV>And I am running this command on a ubuntu 12.04 32-bit.<BR><BR></DIV>Do you have any idea of how I can solve it?<BR><BR></DIV>Thanks once again,Best,<BR>Ricardo<BR><BR>
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<DIV>using the executable "/usr/local/MATLAB/R2012a/toolbox/fieldtrip-20130314/external/dipoli/dipoli"<BR>/tmp/tpd4e382c9_74a1_402d_be1a_6d2c82e749cc.sh: 3: /tmp/tpd4e382c9_74a1_402d_be1a_6d2c82e749cc.sh: /usr/local/MATLAB/R2012a/toolbox/fieldtrip-20130314/external/dipoli/dipoli: not found<BR>Warning: an error ocurred while running dipoli <BR>> In ft_headmodel_dipoli at 201<BR>In ft_prepare_headmodel at 226 <BR><BR>Error using fread<BR>Invalid file identifier. Use fopen to generate a valid file identifier.<BR>Warning: File '/tmp/tp2619f3f3_574d_478a_bfbb_01193b4f8e0c.ama' not found. <BR>> In ft_headmodel_dipoli at 209<BR>In ft_prepare_headmodel at 226 <BR></DIV></DIV></DIV></DIV></DIV></DIV>
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<DIV class=gmail_quote>On 27 March 2013 13:10, Ricardo Moura <SPAN dir=ltr><<A href="mailto:ricardoojm@gmail.com" target=_blank>ricardoojm@gmail.com</A>></SPAN> wrote:<BR>
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<DIV>Dear all<BR>
<DIV>I am creating a BEM model for eeg, following the appropriate tutorial, but I have a problem when preparing the headmodel. The output I have from the ft_prepare_headmodel command does not contain the "mat", and so, when I try to generate the leadfield, it returns an error message due to non existent "mat". I saw that other users had similar problem, but I haven't found a solution though. So, what is wrong with my script?</DIV>
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<DIV>Thanks a lot in advance!</DIV>
<DIV>Best,</DIV>
<DIV>Ricardo</DIV></DIV></DIV>
<DIV><BR><BR><BR><BR>load standard_mri.mat<BR>mri_orig=mri;<BR>disp(mri)<BR><BR>% Segmenting the data<BR>cfg = [];<BR>cfg.output= {'scalp','skull','brain'};<BR>segmentedmri = ft_volumesegment(cfg, mri_orig);<BR>disp(segmentedmri)<BR>save segmentedmri segmentedmri<BR><BR>% MESH <BR>cfg=[];<BR>cfg.tissue={'brain','skull','scalp'};<BR>cfg.numvertices = <A href="tel:%5B3000%202000" target=_blank value="+5530002000">[3000 2000</A> 1000];<BR>bnd=ft_prepare_mesh(cfg,segmentedmri);<BR>disp(bnd(1)) <BR><BR>% Head Model = variavel vol<BR>cfg = [];<BR>cfg.method ='bem_dipoli'; %dipoli singlesphere<BR>vol = ft_prepare_headmodel(cfg, segmentedmri); <BR><BR><BR>>> disp(vol)<BR></DIV>bnd: [1x3 struct]<BR>cond: [0.3300 0.0041 0.3300]<BR>skin_surface: 1<BR>source: 3<BR>type: 'dipoli'<BR>unit: 'mm'<BR>cfg: [1x1 struct]<BR><BR>
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