<div dir="ltr">Dear experts:<div><br></div><div>I was following the tutorial on the whole brain analysis <a href="http://www.fieldtriptoolbox.org/tutorial/networkanalysis/">http://www.fieldtriptoolbox.org/tutorial/networkanalysis/</a>.</div><div><br></div><div>While I got to this block of code that performs parcellation using an atlas for source connectivity:</div><div><br></div><div><pre class="gmail-highlight" style="box-sizing:border-box;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:13.2px;margin-top:0px;margin-bottom:0px;overflow:auto;color:rgb(33,37,41);background:rgb(240,240,240)"><code style="box-sizing:border-box;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;color:inherit;word-break:normal"><span class="gmail-nb" style="box-sizing:border-box;color:rgb(0,112,32)">load</span> <span class="gmail-n" style="box-sizing:border-box">atlas_MMP1</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-mi" style="box-sizing:border-box;color:rgb(64,160,112)">0</span><span class="err" style="box-sizing:border-box;border:1px solid rgb(255,0,0)">_</span><span class="gmail-mi" style="box-sizing:border-box;color:rgb(64,160,112)">4</span><span class="gmail-n" style="box-sizing:border-box">k</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">mat</span><span class="gmail-p" style="box-sizing:border-box">;</span>
<span class="gmail-n" style="box-sizing:border-box">atlas</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">pos</span> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">=</span> <span class="gmail-n" style="box-sizing:border-box">source_conn</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">pos</span><span class="gmail-p" style="box-sizing:border-box">;</span> <span class="gmail-c1" style="box-sizing:border-box;color:rgb(96,160,176);font-style:italic">% otherwise the parcellation won't work</span>

<span class="gmail-n" style="box-sizing:border-box">cfg</span> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">=</span> <span class="gmail-p" style="box-sizing:border-box">[];</span>
<span class="gmail-n" style="box-sizing:border-box">cfg</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">parcellation</span> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">=</span> <span class="gmail-s1" style="box-sizing:border-box;color:rgb(64,112,160)">'parcellation'</span><span class="gmail-p" style="box-sizing:border-box">;</span>
<span class="gmail-n" style="box-sizing:border-box">cfg</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">parameter</span>    <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">=</span> <span class="gmail-s1" style="box-sizing:border-box;color:rgb(64,112,160)">'cohspctrm'</span><span class="gmail-p" style="box-sizing:border-box">;</span>
<span class="gmail-n" style="box-sizing:border-box">parc_conn</span> <span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">=</span> <span class="gmail-n" style="box-sizing:border-box">ft_sourceparcellate</span><span class="gmail-p" style="box-sizing:border-box">(</span><span class="gmail-n" style="box-sizing:border-box">cfg</span><span class="gmail-p" style="box-sizing:border-box">,</span> <span class="gmail-n" style="box-sizing:border-box">source_conn</span><span class="gmail-p" style="box-sizing:border-box">,</span> <span class="gmail-n" style="box-sizing:border-box">atlas</span><span class="gmail-p" style="box-sizing:border-box">);</span>

<span class="gmail-nb" style="box-sizing:border-box;color:rgb(0,112,32)">figure</span><span class="gmail-p" style="box-sizing:border-box">;</span><span class="gmail-nb" style="box-sizing:border-box;color:rgb(0,112,32)">imagesc</span><span class="gmail-p" style="box-sizing:border-box">(</span><span class="gmail-n" style="box-sizing:border-box">parc_conn</span><span class="gmail-o" style="box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="box-sizing:border-box">cohspctrm</span><span class="gmail-p" style="box-sizing:border-box">);</span></code></pre></div><div><br></div><div>The code loads an atlas and replaces the atlas position with the source connectivity position. I am wondering what's the logic behind replacing the atlas.pos with source_conn.pos? This kind of hard-coding replacement seems skeptical and random for me and also the original atlas.pos is very different from source.pos. Is this substitution messing up the parcellation while the labels in the atlas refer to a different position in the source?</div><div><br></div><div>Best regards,</div><div>Andy Liang</div></div>