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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="3" style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif;">Dear Tyler, </font>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
Thank you for your suggestion. </div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
I had checked the option of warping the individual grid to the template grid, but I discarded it, maybe for wrong reasons. From the tutorial, I understand that warping is done via the individual MRI. I have done the segmentation, mesh creation and grid preparation
at the individual level. So the warping of grids seems to redo this segmentation and mesh creation from the individual MRI to get the individual grid and warp it. The function ft_prepare_sourcemodel does not have the option to include the headmodel that I've
already created (in my case, a 3-shell BEM), and that's why I excluded this option.</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
However, maybe I can use the template grid with the BEM like this:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
cfg = [];</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
cfg.grid = template_grid;</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
cfg.inwardshift = 0; </div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
cfg.vol = individual_vol; %result from segmentation and mesh creation</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
warped_grid = ft_prepare_sourcemodel(cfg); </div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
And then create the headmodel:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div>
<div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: medium;"> cfg = [];</span></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.vol = individual_vol;</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.elec = individual_sens;</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.grid = warped_grid;</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.grid.tight = 'yes';</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.reducerank = 'no'; % </font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> cfg.normalize = 'no'; </font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"> leadfield = ft_prepare_leadfield(cfg);</font></div>
</div>
</div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"><br>
</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3">My question is whether this is correct given that warped_grid would be in MNI coordinates, and individual_vol and individual_sens would not. And also, would this mean that the points of the grid
would all be the same for all subjects?</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"><br>
</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3">Best regards,</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3"><br>
</font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" size="3">Laura</font></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif;">
<div style="font-size: 16px; font-family: 'Times New Roman'; color: rgb(0, 0, 0);">
<div id="divRpF584401" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> fieldtrip-bounces@science.ru.nl [fieldtrip-bounces@science.ru.nl] on behalf of Tyler Grummett [tyler.grummett@flinders.edu.au]<br>
<b>Sent:</b> 25 July 2014 02:20<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Group analysis at source level<br>
</font><br>
</div>
<div></div>
<div>
<p style="">Hey laura,<br>
</p>
<p style=""><br>
</p>
<p style="">Im not 100% sure of what I am about to tell you, as I am not an expert, but I think ft_sourceinterpolate is used in tutorials<br>
</p>
<p style="">to display results on an mri model basically. One such tutorial is: </p>
<p style="">http://fieldtrip.fcdonders.nl/tutorial/beamformingextended<br>
</p>
<p style=""><br>
</p>
<p style="">If you want to be consistent over subjects, I would use a sourcemodel when calculating your source variable, like in: <br>
</p>
<p style=""><a href="http://fieldtrip.fcdonders.nl/faq/how_can_i_map_source_locations_between_two_different_representations?s[]=atlas" id="NoLP" target="_blank">http://fieldtrip.fcdonders.nl/faq/how_can_i_map_source_locations_between_two_different_representations?s[]=atlas</a><br>
</p>
<p style="">and: <a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=subject&s[]=grid&s[]=mni" id="NoLP" target="_blank">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=subject&s[]=grid&s[]=mni</a><br>
</p>
<p style=""><br>
</p>
<p style="">I really hope this helps, it helped me :)<br>
</p>
<p style=""><br>
</p>
<p style="">Tyler<br>
</p>
<p style=""><br>
</p>
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<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of Laura Rueda Delgado <Laura.Rueda@faber.kuleuven.be><br>
<b>Sent:</b> Friday, 25 July 2014 1:06 AM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> [FieldTrip] Group analysis at source level</font>
<div> </div>
</div>
<div>
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear fieldtrip users,
<div><br>
</div>
<div>I'm working with source estimations of EEG data. At the moment, I have estimated the sources at the individual level with individual MRIs. I've used ft_sourceinterpolate and ft_volumenormalise to transform the resulting estimation maps into a template
for comparison, and I do this for every subject: </div>
<div><br>
</div>
<div>
<div> cfg = [];</div>
<div> cfg.parameter = 'avg.pow';</div>
<div> source = ft_sourceinterpolate(cfg, source, mri);</div>
<div><br>
</div>
<div> cfg = [];</div>
<div> cfg.template = '\spm8\templates\T1.nii';</div>
<div> cfg.parameter = 'all';</div>
<div> cfg.nonlinear = 'yes';</div>
<div> cfg.coordsys = 'spm';</div>
<div> source = ft_volumenormalise(cfg, source); </div>
</div>
<div><br>
</div>
<div>Once I have the estimated sources for all the subjects, I use ft_sourcestatistics:</div>
<div><br>
</div>
<div>
<div>cfg = [];</div>
<div>cfg.dim = sourcePre_con{1}.dim;</div>
<div>cfg.method = 'montecarlo';</div>
<div>cfg.statistic = 'depsamplesT';</div>
<div>cfg.parameter = 'avg.pow';</div>
<div>cfg.correctm = 'cluster';</div>
<div>cfg.numrandomization = 'all';</div>
<div>cfg.alpha = 0.05;</div>
<div>cfg.tail = 0;</div>
<div>cfg.design(1,:) = [1:num 1:num];</div>
<div>cfg.design(2,:) = [ones(1,num) ones(1,num)*2];</div>
<div>cfg.uvar = 1;</div>
<div>cfg.ivar = 2; </div>
<div>stat = ft_sourcestatistics(cfg,sourcePost_con{:}, sourcePre_con{:});</div>
</div>
<div><br>
</div>
<div>And I get this error:</div>
<div><br>
</div>
<div>
<div><font color="#ff0000">Reference to non-existent field 'pos'.</font></div>
<div><font color="#ff0000"><br>
</font></div>
<div><font color="#ff0000">Error in statistics_wrapper>get_source_avg (line 643)</font></div>
<div><font color="#ff0000"> fprintf('only selecting voxels inside the brain for statistics (%.1f%%)\n', 100*length(varargin{1}.inside)/size(varargin{1}.pos,1));</font></div>
<div><font color="#ff0000"><br>
</font></div>
<div><font color="#ff0000">Error in statistics_wrapper (line 206)</font></div>
<div><font color="#ff0000"> [dat, cfg] = get_source_avg(cfg, varargin{:});</font></div>
<div><font color="#ff0000"><br>
</font></div>
<div><font color="#ff0000">Error in ft_sourcestatistics (line 107)</font></div>
<div><font color="#ff0000"> [stat, cfg] = statistics_wrapper(cfg, varargin{:});</font></div>
</div>
<div><font color="#ff0000"><br>
</font></div>
<div>I check the data structure and the structure of the sources at the individual level, before interpolating and normalising has the pos field, but after these steps, it's gone. How can I work around this error? Do I have to keep the pos field and transform
it according to the template?</div>
<div><br>
</div>
<div>Thank you in advance for your help.</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Laura Rueda</div>
</div>
</div>
</div>
</div>
</div>
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