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<font size="4" class="">Hi Rebecca,</font>
<div class=""><font size="4" class=""><br class="">
</font></div>
<div class=""><font size="4" class="">Just some pointers below. One cannot ‘just’ interpolate one object to another one without considering (and validating) whether,</font></div>
<div class=""><font size="4" class=""><br class="">
</font></div>
<div class=""><font size="4" class="">1) the coordinate system in which the objects are expressed are the same</font></div>
<div class=""><font size="4" class="">2) the objects’ coordinates are expressed in the same metric units (although FT usually tries to check this, and fix it, if possible)</font></div>
<div class=""><font size="4" class="">3) both objects are of a similar ’nature’, i.e. both defined as a 3D volume, or as a point cloud, or as a mesh. (although FT can toggle back and forth, it’s often not desirable)</font></div>
<div class=""><font size="4" class="">4) the atlas you aim to use is appropriate for your data (particularly in light of point 3).</font></div>
<div class=""><font size="4" class=""><br class="">
</font></div>
<div class=""><font size="4" class="">Furthermore, the error you paste is pretty low level and not informative without any additional context. The only thing that I can derive from it, is that the variable ’ sel’ is most likely empty (i.e. contains 0 elements,
which causes the error. What ’sel’ means in this context, and why it is empty in your case is can not be derived. Additional detective work is best done with you, by using the matlab debugger, which allows you to step through the code line-by-line to investigate
the variables in the function’s workspace.</font></div>
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</font></div>
<div class=""><font size="4" class="">Good luck,</font></div>
<div class=""><font size="4" class=""><br class="">
</font></div>
<div class=""><font size="4" class="">Jan-Mathijs</font></div>
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<div class="">On 16 Sep 2020, at 01:08, Rebecca Kenny <<a href="mailto:beckenny@student.ubc.ca" class="">beckenny@student.ubc.ca</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div dir="ltr" class="">Hello Michael,
<div class=""><br class="">
</div>
<div class="">Thank you for your quick response! It seems I am still getting errors.</div>
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</div>
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<div class=""><font color="#ff0000" class="">Index exceeds the number of array elements (0).</font></div>
<div class=""><font color="#ff0000" class=""><br class="">
</font></div>
<div class=""><font color="#ff0000" class="">Error in ft_sourceinterpolate>my_interpn (line 726)</font></div>
<div class=""><font color="#ff0000" class=""> ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num);</font></div>
<div class=""><font color="#ff0000" class=""><br class="">
</font></div>
<div class=""><font color="#ff0000" class="">Error in ft_sourceinterpolate (line 631)</font></div>
<div class=""><font color="#ff0000" class=""> av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel), cfg.interpmethod, cfg.feedback);</font></div>
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<div class="">There should not be anything wrong with my data and I have followed the tutorial to a T. I am not sure what I am missing. I appreciate the help.</div>
<div class=""><br class="">
</div>
<div class="">Rebecca</div>
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<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Sep 15, 2020 at 3:36 PM Michael Glassen - Biomedical Engineer <<a href="mailto:MGlassen@kesslerfoundation.org" class="">MGlassen@kesslerfoundation.org</a>> wrote:<br class="">
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Rebecca,<br class="">
<br class="">
I have run into similar issues, I may be wrong but I believe interpolating the atlas onto your source model will solve this issue. I grabbed some code from one of the tutorials and pasted below, try it out and see if it fixes your error, replacing the atlas
and sourcemodel variables with whatever you’ve named them in your script.<br class="">
<br class="">
Best,<br class="">
Michael Glassen<br class="">
<br class="">
%% <br class="">
cfg = [];<br class="">
cfg.interpmethod = 'nearest';<br class="">
cfg.parameter = 'tissue';<br class="">
newAtlas = ft_sourceinterpolate(cfg, atlas, sourcemodel);<br class="">
<br class="">
<hr style="display:inline-block;width:98%" class="">
<div id="gmail-m_-1782410259123342228divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size:11pt" class=""><b class="">From:</b> fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank" class="">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Rebecca Kenny <<a href="mailto:beckenny@student.ubc.ca" target="_blank" class="">beckenny@student.ubc.ca</a>><br class="">
<b class="">Sent:</b> Tuesday, September 15, 2020 5:54:12 PM<br class="">
<b class="">To:</b> FieldTrip discussion list<br class="">
<b class="">Subject:</b> Re: [FieldTrip] EEG connectivity analysis - error with ft_sourceparcellate in whole brain connectivity tutorial</font>
<div class=""> </div>
</div>
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<div dir="ltr" class="">Hello Jan-Mathijs,
<div class=""><br class="">
</div>
<div class="">Thank you very much for your reply! It seems to have worked and I am really appreciative. I now have a new error that maybe you can help with. Would this be because of the atlas I chose?</div>
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<div class="">cfg = [];</div>
<div class=""> cfg.parcellation = 'tissue';</div>
<div class=""> cfg.parameter = 'cohspctrm';</div>
<div class=""> parc_conn = ft_sourceparcellate(cfg, source_conn, atlas);</div>
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<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">there are in total 4050 positions, 2015 positions are inside the brain, 701027 positions have a label</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">0 of the positions inside the brain have a label</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">The logical indices contain a true value outside of the array bounds.</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class=""><br class="">
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class=""><font color="#ff0000" class="">Error in ft_sourceparcellate (line 172)</font></blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class=""><font color="#ff0000" class=""> fprintf('%d of the labeled positions are inside the brain\n', sum(source.inside(seg(:)~=0)));</font></blockquote>
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<div class="">Thank you,</div>
<div class="">Rebecca</div>
<div class=""><br class="">
</div>
</div>
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<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Sep 14, 2020 at 10:50 PM Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank" class="">jan.schoffelen@donders.ru.nl</a>> wrote:<br class="">
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<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Rebecca,
<div class=""><br class="">
</div>
<div class="">The atlas needs to be represented as a proper atlas, also known as a ‘parcellation’. Unless you know what you’re doing, this can only be achieved if the specified atlas is either in a well defined mat-file, or if the atlas is created (i.e. read
from file + some additional wizardry applied to those data) by ft_read_atlas. I suspect that you did not do atlas = ft_read_atlas(‘AllAreas_v17_MPM.mat’); in order to create the atlas variable.</div>
<div class=""><br class="">
</div>
<div class="">Also, note that ft_sourceparcellate will try and make the parcellation according to the information in the named <cfg.parcellation> field. After calling ft_read_atlas for the AllAreas_v17_MPM file, this parcellation is defined in the (confusingly)
’tissue’ field, so cfg.parcellation should be ’tissue’.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
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<blockquote type="cite" class="">
<div class="">On 14 Sep 2020, at 20:41, Rebecca Kenny <<a href="mailto:beckenny@student.ubc.ca" target="_blank" class="">beckenny@student.ubc.ca</a>> wrote:</div>
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<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">Hello,<br class="">
<br class="">
I am attempting to run connectivity analysis on resting-state EEG data. <b class="">
My goal of source space analysis is to run <i class="">ft_networkanalysis</i> and extract graph theory variables. </b>I am following the "whole-brain connectivity and network analysis" tutorial. I believe I have successfully navigated the tutorial (after importing
my cleaned data from EEGlab) until I experience errors when I get to the 'connectivity analysis and parcellation'.<br class="">
<br class="">
I can't find the atlas_MMP1.0_4k.mat file so I tried to use AllAreas_v17.mat.<br class="">
<br class="">
</div>
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<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> % compute connectivity</div>
</blockquote>
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<div class=""> cfg = [];</div>
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<div class=""> cfg.method ='coh';</div>
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<div class=""> cfg.complex = 'absimag';</div>
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<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> source_conn = ft_connectivityanalysis(cfg, source);</div>
</blockquote>
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<div class=""> </div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> load AllAreas_v17.mat;</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> atlas.pos = source_conn.pos; </div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> </div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> cfg = [];</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> cfg.parcellation = 'parcellation';</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> cfg.parameter = 'cohspctrm';</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> parc_conn = ft_sourceparcellate(cfg, source_conn, atlas);</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""><br class="">
</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class=""> figure;imagesc(parc_conn.cohspctrm);</div>
</blockquote>
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</div>
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<div class="">Error using ft_checkdata (line 528)</div>
</blockquote>
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<div class="">This function requires parcellation data as input, see ft_datatype_parcellation.</div>
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<div class=""><br class="">
</div>
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<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class="">Error in ft_sourceparcellate (line 97)</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class="">parcellation = ft_checkdata(parcellation, 'datatype', 'parcellation', 'parcellationstyle', 'indexed');</div>
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<div class=""><br class="">
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<div class="">
<div class="">If there is an email thread already, please direct me to the proper post. </div>
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<div class="">I appreciate any help. I have been stuck at this part for a while and would love to move through my analysis.</div>
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<div class="">Thank you,</div>
<div class="">Rebecca </div>
<div class=""><br class="">
</div>
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