<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Jan-Mathijs,<div class="">Thank you very much for your reply! I have been halted in this problem for a few days… And I am really looking forward urgently to get the source localization result. So I am sorry to bother you again!</div><div class="">But there is still something wrong with followed steps in this page.</div><div class="">1. The built of volume conduction model. I noticed that it is required to create the volume model with same coordinate system as MEG sensor positions were defined. The ‘or-nomask.mgz’ file was asked to provide again to be used as anatomical data. I chose to replace this file with ‘orig.mgz’ first, but I got bad outcome as displayed below:</div><div class=""><img apple-inline="yes" id="E4558D98-FCF2-45EA-B345-2062101FC012" height="307" width="339" apple-width="yes" apple-height="yes" src="cid:54C2AA0E-40B9-4DD0-85BC-ADF0D39406C3" class=""></div><div class="">the code I applied was copied from the web:</div><div class=""><pre class="code" style="padding: 0.5em; margin-top: 0px; margin-left: -10px; border: 1px dashed rgb(204, 204, 204); overflow: hidden; font-family: Consolas, 'Andale Mono', Menlo, Monaco, monospace; background-color: rgb(247, 249, 250); white-space: pre-wrap; width: 640px; text-align: justify;">mri_nom = ft_read_mri('orig.mgz');
cfg = [];
cfg.coordsys = 'spm';
cfg.output = {'brain'};
seg = ft_volumesegment(cfg, mri_nom);
seg = ft_convert_units(seg,'cm');
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg,seg);
vol.bnd = ft_transform_geometry(T, vol.bnd);
save vol vol;</pre></div><div class=""><br class=""></div><div class="">So should I use the mri data with ctf coordinate system to build the model and then transform it to spm system with the ’T’ metric?</div><div class=""><br class=""></div><div class="">2. When I did Forward solution, I could not find sourcespace.pnt, parameters I got in the sourcespace as below:</div><div class=""> <img apple-inline="yes" id="DAE3A634-AFB0-42CC-840A-52749BE42D58" height="125" width="253" apple-width="yes" apple-height="yes" src="cid:53FEE89D-0C04-4D88-96B9-B5622C75A6EC" class=""></div><div class="">what is the definition of ‘.pnt’? Why it was lost in my sourcespace data? </div><div class=""><br class=""></div><div class="">Thank you for your help!</div><div class=""><br class=""></div><div class="">Best</div><div class="">Runnan</div><div class=""><div><blockquote type="cite" class=""><div class="">On Mar 14, 2016, at 16:40, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Runnan,
<div class=""><br class="">
</div>
<div class="">Sorry for the confusion. The part of the documentation you are working with is currently being improved, but not finalized yet. </div>
<div class="">In particular, the part you refer to ‘Source model: co-registration of the source space to the sensor-based coordinate system’ needs a heavy update. I would assume that you have done the tutorial up until there. In particular, if you have done
the preprocessing of the anatomical MRI, where you have created 2 transformation matrices (using the same anatomical volume), you’re almost there. So please forget about the orig.mgz, either nomask or not, and please be a bit patient until we (i.e. I) find
time to update the documentation.</div>
<div class=""><br class="">
</div>
<div class="">This is how you get the appropriate coregistration:</div>
<div class=""><br class="">
</div>
<div class="">(Note: I assume that all the objects are defined in ‘mm’, otherwise it won’t work. To get all things in ‘mm’, use ft_convert_units).</div>
<div class=""><br class="">
</div>
<div class="">Preliminaries:</div>
<div class="">-we know how to get from an arbitrary voxel-space to the sensor-based coordinate system: transform_vox2ctf</div>
<div class="">-we know how to get to the ‘mni’ coordinate system from the same arbitrary voxel-space: transform_vox2spm</div>
<div class="">-we know that the sourcespace is expressed in the ‘mni’ coordinate system (check the units, is it mm?)</div>
<div class=""><br class="">
</div>
<div class="">Based on the first two points above, we can easily construct a transformation matrix that goes from ‘mni’ to ‘ctf’:</div>
<div class=""><br class="">
</div>
<div class="">T = transform_vox2ctf/transform_vox2spm</div>
<div class=""><br class="">
</div>
<div class="">We can now use T to transform the sourcespace:</div>
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</div>
<div class="">sourcespace = ft_transform_geometry(T, sourcespace);</div>
<div class=""><br class="">
</div>
<div class="">I am pretty sure that this will do the trick.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
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<div class="">
<blockquote type="cite" class="">
<div class="">On 13 Mar 2016, at 13:20, Harold Cavendish <<a href="mailto:harold.cav89@gmail.com" class="">harold.cav89@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Dear Runnan,
<div class=""><br class="">
</div>
<div class="">I'd be happy to help, but sadly, I have no experience with FreeSurfer and skipped that portion of the tutorial entirely (instead, I used files from fieldtrip/template).</div>
<div class=""><br class="">
</div>
<div class="">However, using just common sense, I believe there's an error in the tutorial because orig-nomask.mgz is mentioned for the first time where you need to load it but it isn't present in any of the outputs or in the Subject01 directory. I believe
it's just a renamed copy of orig.mgz which is created as explained in the tutorial.</div>
<div class=""><br class="">
</div>
<div class="">As far as I understand, you take an anatomical MRI image (e.g. Subject01.mri), use FT to do some preprocessing and get Subject01.mgz (a FreeSurfer-compatible format), then do some segmentation and get Subject01masked.mgz, then do some conversion
in FreeSurfer and transform those two into orig.mgz and brainmask.mgz respectively, and to make it even more convoluted, some filled.mgz pops up as well. To be honest, I don't follow… I have zero experience with FreeSurfer as well as MRI/fMRI analysis.</div>
<div class=""><br class="">
</div>
<div class=""><b class="">Briefly, try using orig.mgz instead of orig-nomask.mgz whenever you need to use ft_read_mri('orig-nomask.mgz'). If it doesn't do the job, hopefully someone else will come to the rescue.</b></div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra">Best regards,</div>
<div class="gmail_extra">Harold</div>
<div class="gmail_extra"><br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 12 March 2016 at 01:02, <span dir="ltr" class=""><<a href="mailto:runna90@126.com" target="_blank" class="">runna90@126.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="auto" class="">
<div class=""><span class=""></span></div>
<div class="">
<div class=""><span class=""></span></div>
<div class=""><span class="">Dear Harold,</span><br class="">
<span class="">I am very sorry that I am not writing to reply your question but to request you something about minimum norm estimate because I am a rather new fieldtripper. I noticed that you have got results applying MNE, thus I think you must be more experienced!
I followed the tutorial at </span><a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate" target="_blank" class="">http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate</a> and did source reconstruction with MEG data acquired from ctf
275 system. But I got stuck in here</div>
<h4 style="text-align:start;padding:0px;margin:1em 0px 0em;clear:left;line-height:1em" class="">
<a name="-1172118713_source_modelco-registration_of_the_source_space_to_the_sensor-based_head_coordinate_system" style="padding:0px;margin:0px;background-color:rgba(255,255,255,0)" class=""><font class="">. Source model: Co-registration of the source space
to the sensor-based head coordinate system, </font></a></h4>
<div class=""><span style="background-color:rgba(255,255,255,0)" class="">I could not find the file named ‘orig-nomask.mgz’ under the mir folder. Would you tell me in which step should this file be created? And how to create this file?</span></div>
<div class=""><br class="">
Best regards,<br class="">
<span class=""></span><br class="">
Runnan
<div class="">
<div class="h5"><br class="">
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</div>
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<blockquote type="cite" class=""><span class="">在 2016年3月10日，08:40，Harold Cavendish <<a href="mailto:harold.cav89@gmail.com" target="_blank" class="">harold.cav89@gmail.com</a>> 写道：</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Dear FieldTrip users,</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">I have a few questions regarding source localisation and statistics:</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">1. Suppose I'm doing source reconstruction of ERP using minimum-norm estimate; one condition, multiple subjects. I'm using ft_sourceanalysis() and getting rather meaningful results which I visualise via ft_plot_mesh().</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">What is the validity of this result? I understand there are many individual dipoles spread over the cortical sheet and we're estimating best fit to the data given the conductance model while minimising overall
power, but what does this actually tell us? If I find an area with higher power, what conclusions can I draw?</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">2. Can I compute a correlation between the result in the source space and a behavioural variable? Perhaps even specify a region of interest? If yes, is this approach considered to be valid?</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">I want to see if e.g. the power of the reconstructed activity in the source space averaged over a time window correlates with my behavioural variable.</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Thank you!</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class=""></span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Best regards,</span><br class="">
</blockquote>
<blockquote type="cite" class=""><span class="">Harold</span><br class="">
</blockquote>
</div>
</div>
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