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Hi Julian,<br><br>thank you for response. That did indeed solve the problem.<br>I had commented out the section where everything is converted<br>from mm to cm.<br><br>Now the grid is at least on the same scale as the head model.<br>However, when I compare the template grid (Figure1) with<br>the individual grid (Figure6) it seems as if there is still a difference.<br><br>Is this normal and a consequence of the warping or should the<br>plot look different?<br><br>Best, Fred<br><br>-- <br>Frédéric Roux, PhD student<br>Department of Neurophysiology<br>Max Planck Institute for Brain Research<br>D-60529 Frankfurt am Main<br>Frederic.Roux@brain.mpg.de<br>+49(0)69630183225<br><br><br><br><br><div><div id="SkyDrivePlaceholder"></div>> From: fieldtrip-request@donders.ru.nl<br>> Subject: fieldtrip Digest, Vol 16, Issue 51<br>> To: fieldtrip@donders.ru.nl<br>> Date: Thu, 29 Mar 2012 17:46:09 +0200<br>> <br>> Send fieldtrip mailing list submissions to<br>> fieldtrip@donders.ru.nl<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> or, via email, send a message with subject or body 'help' to<br>> fieldtrip-request@donders.ru.nl<br>> <br>> You can reach the person managing the list at<br>> fieldtrip-owner@donders.ru.nl<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of fieldtrip digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. alignment channel array, head model & individual grid<br>> (Frederic Roux)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Thu, 29 Mar 2012 17:45:52 +0200<br>> From: Frederic Roux <fredericroux@hotmail.de><br>> To: <fieldtrip@donders.ru.nl><br>> Subject: [FieldTrip] alignment channel array, head model & individual<br>> grid<br>> Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480@phx.gbl><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> <br>> Dear all,<br>> <br>> I have trouble finding the right alignment for my head models and individual grids<br>> with the MEG channel array.<br>> <br>> The code I use is the following:<br>> <br>> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');<br>> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');<br>> ft_defaults;<br>> <br>> spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';<br>> spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';<br>> <br>> rmpath(spm2path,spm8path);<br>> <br>> <br>> mri = ft_read_mri('ID_V2.mri');<br>> <br>> cfg = [];<br>> cfg.coordsys = 'ctf';<br>> seg = ft_volumesegment(cfg,mri);<br>> <br>> cfg = [];<br>> hdm = ft_prepare_singleshell(cfg,seg);<br>> <br>> cfg = [];<br>> cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';<br>> cfg.coordsys = 'ctf';<br>> cfg.nonlinear = 'no';<br>> <br>> norm = ft_volumenormalise(cfg,mri);<br>> <br>> load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8<br>> <br>> grid = [];<br>> grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;<br>> grid.inside = template_gird.inside;<br>> grid.outside = template_grid.outside;<br>> <br>> transfrom_ctf2spm = norm.cfg.final;<br>> <br>> figure;<br>> hold on;<br>> ft_plot_sens(ft_read_sens('ID.ds'));<br>> ft_plot_vol(hdm);<br>> ft_plot_mesh(grid.pos(grid.inside,:));<br>> <br>> <br>> Would be great if you could help me to figure out what is going wrong here.<br>> <br>> Best,<br>> Fred<br>> <br>> <br>> -- <br>> Fr?d?ric Roux, PhD student<br>> Department of Neurophysiology<br>> Max Planck Institute for Brain Research<br>> D-60529 Frankfurt am Main<br>> Frederic.Roux@brain.mpg.de<br>> +49(0)69630183225<br>> <br>> <br>> <br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120329/cdd714b6/attachment.html><br>> -------------- next part --------------<br>> A non-text attachment was scrubbed...<br>> Name: individual_grid_sensor_array_headmodel2.jpg<br>> Type: image/jpeg<br>> Size: 43058 bytes<br>> Desc: not available<br>> URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120329/cdd714b6/attachment.jpg><br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> fieldtrip mailing list<br>> fieldtrip@donders.ru.nl<br>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>> <br>> End of fieldtrip Digest, Vol 16, Issue 51<br>> *****************************************<br></div> </div></body>
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