<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div>I am still stuck with the correspondence of the source space with parcellation. </div></div></div></blockquote><div><br></div><div>In general, a source space takes the high resolution mesh (~100k verts) and subselects a small subset of them (~10k or less). The subset is stored in `src[0]['vertno']` for the left hemi and `src[1]['vertno']` for the right.</div><div><br></div><div>Parcellations are generally defined (by FreeSurfer) on the entire high resolution cortical surface, and thus should contain many more points than our decimated source space.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div>So, for a given source space (e.g. ico 4, 2562 sources per hemisphere) I would expect to find the vertices 0...2561 in the parcellation.</div></div></div></blockquote><div><br></div><div>The parcellation can have holes. In the case of "aparc" the medial wall vertices are missing:</div><div></div><div class="markdown-here-wrapper" style=""><pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline;white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">>>> import surfer
>>> brain = surfer.Brain('fsaverage', 'lh', 'white', views='med')
>>> brain.add_annotation('aparc', borders=False)
</code></pre><div title="MDH:PGRpdj5gYGA8L2Rpdj48ZGl2PiZndDsmZ3Q7Jmd0OyBpbXBvcnQgc3VyZmVyPC9kaXY+PGRpdj4m
Z3Q7Jmd0OyZndDsgYnJhaW4gPSBzdXJmZXIuQnJhaW4oJ2ZzYXZlcmFnZScsICdsaCcsICd3aGl0
ZScpPGJyPiZndDsmZ3Q7Jmd0OyBicmFpbi5hZGRfYW5ub3RhdGlvbignYXBhcmMnLCBib3JkZXJz
PUZhbHNlKTxicj48L2Rpdj48ZGl2PmBgYDwvZGl2PjxkaXY+PC9kaXY+" style="height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0em;padding:0;margin:0"></div></div><div><div><img src="cid:ii_k086ra6d1" alt="Screenshot from 2019-09-06 09-58-16.png" width="216" height="224" style="margin-right: 0px;"><br></div></div><div><br></div><div>Also keep in mind that the decimated source space vertices being numbered 0 to 2561 is a property unique to `fsaverage` (and how its spherical mesh is arranged), in general for other subjects these can and will be integers spanning the whole ~100k brain space.</div><div><br></div><div>Eric</div><div><br></div></div></div>