<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap:break-word"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Dear Fieldtrippers,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">I'm using the VTPM atlas to define masks for all the visual regions described in the paper (Wang et al. 2014, <a href="https://academic.oup.com/cercor/article-lookup/doi/10.1093/cercor/bhu277">https://academic.oup.com/cercor/article-lookup/doi/10.1093/cercor/bhu277</a>). However, there seem to be no entries corresponding to the left IPS5.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><i>% load atlas</i></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><i>atl = ft_read_atlas('~/Documents/fieldtrip/vtpm/vtpm.mat');</i></div><i>atl = ft_convert_units(atl, 'cm');</i><div><i><br></i></div><div><i>% add mni coordinates</i></div><div><div><i>[ax, ay, az] <span class="Apple-tab-span" style="white-space:pre"> </span>= voxelcoords(atl.dim, atl.transform);</i></div><div><i>atl.pos <span class="Apple-tab-span" style="white-space:pre"> </span>= [ax(:) ay(:) az(:)];</i></div><div><i><br></i></div><div><i>% make a binary mask for this ROI</i></div><div><div><i>roi_idx <span class="Apple-tab-span" style="white-space:pre"> </span>= find(strcmp(lower(atl.tissuelabel), 'IPS5'));</i></div><div><div><i>roi_mask <span class="Apple-tab-span" style="white-space:pre"> </span>= ismember(atl.tissue, roi_idx);</i></div><div><i><br></i></div><div><i>% mask the voxels on the right side of the brain</i></div><div><i>rightidx <span class="Apple-tab-span" style="white-space:pre"> </span>= find(atl.pos(:, 1) > 0); </i></div><div><i>roi_mask(rightidx) <span class="Apple-tab-span" style="white-space:pre"> </span>= 0;</i></div><div><br></div><div>Now, sum(roi_mask(:)) = 0. This procedure of separating out the left and right regions works fine for all other regions in the atlas, as well as the right IPS5. </div><div><br></div><div>The description on <a href="http://www.fieldtriptoolbox.org/template/atlas">http://www.fieldtriptoolbox.org/template/atlas</a> says "The version of the atlas included with FieldTrip was created by transforming data into standardized space using surface-based anatomical registration approaches." Is there any information available on the exact code that was used to go from this original file <a href="http://scholar.princeton.edu/napl/resources">http://scholar.princeton.edu/napl/resources</a> to the mat-file in FieldTrip, so that I can check where in the process the left IPS5 gets lost?</div><div><br></div><div>Thanks!</div><div><br></div><div id="bloop_sign_1499675349525215232" class="bloop_sign"><div>—</div><div>Anne E. Urai, MSc</div><div>PhD student | Institut für Neurophysiologie und Pathophysiologie</div><div>Universitätsklinikum Hamburg-Eppendorf | Martinistrasse 52, 20246 | Hamburg, Germany</div><div><a href="http://www.anneurai.net">www.anneurai.net</a> / @AnneEUrai</div></div></div></div></div></body></html>