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Hi Andrew,</div>
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What’s the point in doing the second, headshape based alignment? I suppose that the template electrode positions are defined in a different coordinate system than ‘spm’?</div>
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If so, be aware that probably these template positions do not nicely match the reconstructed headsurface from the template MRI, so you need to do the headshape based alignment by hand, since the automatic icp algorithm probably will get caught in an inappropriate
local minimum. As long as you don’t rotate around the z-axis, I would assume that the ‘rotation’ would go away. </div>
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Note, that the rotation of the image itself (as per ft_volumereslice) is not the problem, but the fact that it is rotated probably is, because that suggest that your coregistration between anatomy and electrodes does not make sense.</div>
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Best,</div>
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Jan-Mathijs</div>
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J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<blockquote type="cite" class="">
<div class="">On 06 Mar 2017, at 19:04, Andrew Chang <<a href="mailto:changa5@mcmaster.ca" class="">changa5@mcmaster.ca</a>> wrote:</div>
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<div dir="ltr" class="">Dear Fieldtrip users,
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<div class="">I am following the tutorial (<a href="http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting" class="">http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting</a>) to work on coregistering the anatomical MRI (using colin27 template)
to the EEG coordinate system, and then reslicing the MRI on to a cubic grid. However, I found that the ft_volumereslice rotates the MRI image, which seems weird.</div>
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<div class="">This is the sourceplot of the realigned MRI (from the 'mri_realigned2' variable, see the code below):</div>
<div class=""><span id="cid:ii_15aa4aab1e042fc6"><realigned.jpg></span><br class="">
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<div class="">However, this is the sourceplot of the resliced MRI, which was rotated in 3 dimensions (from the 'mri_resliced' variable, see the code below):</div>
<div class=""><span id="cid:ii_15aa4ba9c2b609f8"><resliced.jpg></span><br class="">
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<div class="">I found that this rotation effect can be modulated by adjusting the parameters [rotation, scale, translate] on xyz dimensions, when I use the 'headshap' method for ft_volumerealign (see the code below). However, the effect of adjusting these parameters
seems not to be linear or intuitive at all, and I cannot find the best combination to fix the rotation problem. </div>
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<div class="">Any advice or help would be much appreciated! Thank you all in advance!<br class="">
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<div class="">Here is the .mat file of what I have done: <a href="https://www.dropbox.com/s/viazz1vaq8gjyqb/fixingRotationMRI.mat?dl=0" class="">https://www.dropbox.com/s/viazz1vaq8gjyqb/fixingRotationMRI.mat?dl=0</a></div>
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<div class="">Here is my code</div>
<div class=""><font face="monospace, monospace" class="">%% load MRI</font></div>
<div class=""><font face="monospace, monospace" class="">[mri_orig] = ft_read_mri('colin27_t1_tal_lin.nii');<br class="">
</font></div>
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</font></div>
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<div class=""><font face="monospace, monospace" class="">%% load elec locations</font></div>
<div class=""><font face="monospace, monospace" class="">% I do not have the channel location or the headshape file, so I use a template cap to build the channel locations and headshape</font></div>
<div class=""><font face="monospace, monospace" class="">load('chanCfg')</font></div>
<div class=""><font face="monospace, monospace" class="">sphcoor = [Theta,Phi]';</font></div>
<div class=""><font face="monospace, monospace" class="">cartcoor = elp2coor(sphcoor,10)'; % converting theta/phi coorfinates into xyz</font></div>
<div class=""><font face="monospace, monospace" class="">elec.elecpos = cartcoor;</font></div>
<div class=""><font face="monospace, monospace" class="">elec.chanpos = cartcoor;</font></div>
<div class=""><font face="monospace, monospace" class="">elec.label = ChannelName; % 'ChannelName' is a cell array of channel labels</font></div>
<div class=""><font face="monospace, monospace" class="">elec.unit = 'cm';</font></div>
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</font></div>
<div class=""><font face="monospace, monospace" class="">shape.pos = elec.elecpos;</font></div>
<div class=""><font face="monospace, monospace" class="">shape.label = elec.label;</font></div>
<div class=""><font face="monospace, monospace" class="">shape.unit = elec.unit ;</font></div>
<div class=""><font face="monospace, monospace" class="">shape.coordsys = 'spm';</font></div>
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</font></div>
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<div class=""><font face="monospace, monospace" class="">%% Coregister the anatomical MRI to the EEG coordinate system</font></div>
<div class=""><font face="monospace, monospace" class="">cfg = [];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.method = 'interactive';</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.coordsys = 'spm';</font></div>
<div class=""><font face="monospace, monospace" class="">[mri_realigned1] = ft_volumerealign(cfg, mri_orig);</font></div>
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</font></div>
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<div class=""><font face="monospace, monospace" class="">cfg = [];</font></div>
<div class=""><font face="monospace, monospace" class="">mri_realigned2 = [];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.method = 'headshape';</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.coordsys = 'spm';</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.headshape = shape;</font></div>
<div class=""><font face="monospace, monospace" class="">[mri_realigned2] = ft_volumerealign(cfg, mri_orig);<br class="">
</font></div>
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<div class=""><font face="monospace, monospace" class="">% key in the following parameter for controlling the alignment</font></div>
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<div class="">% rotation: [0,0,0.5]</div>
<div class="">% scale: [0.95, .8, .8]</div>
<div class="">% translate: [0, 15, 0]</div>
</font></div>
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</font></div>
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<div class=""><font face="monospace, monospace" class="">cfg = [];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.resolution = 1;</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.xrange = [-100 100];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.yrange = [-110 110];</font></div>
<div class=""><font face="monospace, monospace" class="">cfg.zrange = [-50 120];</font></div>
<div class=""><font face="monospace, monospace" class="">mri_resliced = ft_volumereslice(cfg, mri_realigned2);</font></div>
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Best,</div>
<div class="">Andrew<br clear="all" class="">
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-- <br class="">
<div class="gmail-m_-7274084066534655969gmail_signature">
<div dir="ltr" class="">Andrew Chang, Ph.D. Candidate<br class="">
Vanier Canada Graduate Scholar<br class="">
<a href="http://changa5.wordpress.com/" target="_blank" class="">http://changa5.wordpress.com/</a><br class="">
<br class="">
Auditory Development Lab<br class="">
Department of Psychology, Neuroscience & Behaviour<br class="">
McMaster University</div>
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