<div>Hi mailing list,</div><div><br></div><div>I'm still struggling with the conversion of coordinates between source and interpolated source space. </div><div>For example, if i have the position of a single grid point how do i get the corresponding voxel in the interpolated source structure. Or the other way around, how to get the grid point which corresponds to a voxel (e.g the max voxel) in the interpolated source structure.</div>
<div><br></div><div>I think this should be a common problem when working with virtual electrodes, shouldn't it?</div><div><br></div><div>To make things easier i put together a example with the data from the source tutorial where i tried to calculated the grid pos of the max voxel in the interpolated source. </div>
<div><br></div><div><div><div>clear all;</div><div>load sourcePost_nocon; % source structure from tutorial</div><div>mri = ft_read_mri('Subject01.mri'); % mri of subject01 from tutorial</div><div><br>
</div><div>sourceNAI = sourcePost_nocon;</div><div>sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./ sourcePost_nocon.avg.noise;</div><div>sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that to let </div><div>
<br></div><div>cfg = [];</div><div>cfg.downsample = 2;</div><div>cfg.parameter = 'avg.pow';</div><div>sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri);</div><div><br></div><div>% Find position of max activity </div>
<div>[dum, maxindx] = max(sourceNAIInt.avg.pow(:));</div><div>[xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx);</div><div>posInt=[xi, yi, zi];</div><div><br></div><div>% Plot interpolated source with position of max activity</div>
<div>cfg = [];</div><div>cfg.method = 'ortho';</div><div>cfg.funparameter = 'avg.pow';</div><div>cfg.locationcoordinates = 'voxel';</div><div>cfg.location = posInt; % location of max activity is marked correctly.</div>
<div>figure;</div><div>ft_sourceplot(cfg,sourceNAIInt);</div><div><br></div><div>% Transform coordinate back to uninterpolated source???</div><div>dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous'); </div>
<div><br></div><div><br></div><div>% Plot uninterpolated source with position aquired from interpolated source</div><div>cfg = [];</div><div>cfg.method = 'ortho';</div><div>cfg.funparameter = 'avg.pow';</div>
<div>cfg.locationcoordinates = 'voxel';</div><div>cfg.location = dpos; % unfortunately this coordinate is obviously wrong!!! WHY?</div><div>figure;</div><div>ft_sourceplot(cfg,sourceNAI);</div></div>
</div><div><br></div><div><br></div><div>Unfortunately the solution of Jan Mathijs did not work, nor did mine :(</div><div><br></div><div>Any ideas???</div><div><br></div><div>Cornelius</div><div><br></div><br><br><div class="gmail_quote">
2012/6/28 jan-mathijs schoffelen <span dir="ltr"><<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Cornelius,<div><br></div><div>Probably you should use: cfg.locationcoordinates to be 'head'.</div>
<div><br></div><div>Best,</div><div><br></div><div>JM</div><div><div><div><br><div><div>On Jun 28, 2012, at 11:19 AM, Cornelius Abel wrote:</div><br><blockquote type="cite"><div>Hi jan mathijs, hello mailing list,</div>
<div><br></div><div>thanks for your answer. I think i got your idea with finding the minimum in this squared differences. This should the work with positions of any scaling, right?</div>
<div>However it gives me strange results when trying to get voxel indices in the "raw" source using voxel indices aquired from interpolated source.</div><div>But even using the ctf coordinates in mm doesn't work.</div>
<div><br></div><div>Here is a short script showing what i did, i also attached the necessary mat files.</div><div><br></div><div>greetings, Cornelius</div><div><br></div><div><br></div><div><div>clear all;</div><div>load testdata.mat;</div>
<div><br></div><div>% Interpolate source on anatomy</div><div>cfg = [];</div><div>cfg.parameter = 'avg.itc';</div><div>cfg.interpmethod = 'linear';</div><div>sourceInt = ft_sourceinterpolate(cfg, source,mri);</div>
<div><br></div><div>% Find position of max voxel in interpolated source</div><div>[maxval, maxindx] = max(sourceInt.avg.itc(:));</div><div>[x,y,z]=ind2sub(size(sourceInt.avg.itc),maxindx);</div><div>pos=[x y z];</div><div>
<br></div><div>% plot this position in interpolated source </div><div>figure;</div><div>cfg = [];</div><div>cfg.method = 'ortho';</div><div>cfg.funparameter = 'avg.itc';</div><div>cfg.locationcoordinates = 'voxel';</div>
<div>cfg.location = pos;</div><div>ft_sourceplot(cfg, sourceInt); </div><div><br></div><div>% Calculate respective position in 'raw' source struct</div><div>dpos = source.pos - repmat(pos, size(source.pos,1),1);</div>
<div>[m,ind] = min(sum(dpos.^2,2));</div><div>spos=source.pos(ind,:);</div><div><br></div><div>% Plot position in 'raw' source.</div><div>% This gives not the position of max activity!!!</div><div>figure;</div><div>
cfg = [];</div><div>cfg.method = 'ortho';</div><div>cfg.funparameter = 'avg.itc';</div><div>cfg.locationcoordinates = 'voxel';</div><div>cfg.location = spos;</div><div>ft_sourceplot(cfg, source); </div>
</div><div><br></div><br><br><div class="gmail_quote">2012/6/27 jan-mathijs schoffelen <span dir="ltr"><<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Cornelius,<div><br></div><div>There is no need to 'uninterpolate' because the coordinates are already expressed in the correct coordinate system. What you probably want is to find the index to the voxel in the original source-structure closest to your 'hotspot' in the interpolated image.</div>
<div>This can be achieved by something like this:</div><div><br></div><div>write down the coordinates of your favourite position in the interpolated image (in world coordinates, here I assume that you are still in MEG coordinate system and have not normalized to MNI space), call this pos</div>
<div><br></div><div>pos = pos./10 (from mm to cm)</div><div><br></div><div>dpos = source.pos - repmat(pos, size(source.pos,1),1);</div><div>[m,ind] = min(sum(dpos.^2,2));</div><div><br></div><div>source is the original source structure.</div>
<div>ind is the index you are looking for.</div><div><br></div><div>If you have interpolate to the MNI-template grid you need to replace the source.pos with the set of grid positions from your template grid (i.e. expressed in MNI coordinates).</div>
<div><br></div><div><br></div><div>Cheers,</div><div><br></div><div>JM</div><div><br></div><div><br><div><div><div><div>On Jun 27, 2012, at 5:26 PM, cornelius abel wrote:</div><br></div></div><blockquote type="cite">
<div><div><div>Hello,<br><br>does anybody know how to get the uninterpolated source position giving the coordinates aquired after interpolation with an anatomy.<br>In principle i want to get an individual source time course at the position i picked from the interpolated grand average source plot. Therfore i need the corresponding filter and its position in the source structure.<br>
<br>I tried to get the position by applying the inverse transformation matrix of the used anatomy like:<br>pos_before_interpolation=warp_apply(inv(anatomy.transform), position_after_interpolation);<br><br>but that did not give usefull results :(<br>
<br>Any ideas how it could be done?<br><br>Greetings, Cornelius<br><br></div></div>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
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<div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div>
<div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: <a href="tel:%2B31-24-3614793" value="+31243614793" target="_blank">+31-24-3614793</a></div>
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<div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div>
<div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: <a href="tel:%2B31-24-3614793" value="+31243614793" target="_blank">+31-24-3614793</a></div>
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