<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">Hi Tvetan,</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">Thanks for your help. </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"><pre style="white-space:pre-wrap"><div id="bloop_customfont" style="font-family:Helvetica,Arial;white-space:normal;margin:0px"><pre style="white-space:pre-wrap">Dear Anne,<i>
</i>><i> 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?
</i>this information was provided by the principle investigator of the paper. You might ask the corresponding author for further details on this.
Best
tzvetan</pre><div>I've been in touch with Dr. Liang Wang (first author on the paper), but he could only point me to the original NIfTI files on the website which have been converted in AFNI. Do you know by any chance which author provided the mat file, so I can work from the code they used? </div></div></pre></div> <div>Best,</div><br> <div id="bloop_sign_1500360128530472960" 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 class="airmail_ext_on" style="color:black"><br>From: <span style="color:black">Anne Urai</span> <a href="mailto:anne.urai@gmail.com"><anne.urai@gmail.com></a><br>Reply: <span style="color:black">Anne Urai</span> <a href="mailto:anne.urai@gmail.com"><anne.urai@gmail.com></a><br>Date: <span style="color:black">10 July 2017 at 10:38:59</span><br>To: <span style="color:black"><a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a></span> <a href="mailto:fieldtrip@science.ru.nl"><fieldtrip@science.ru.nl></a><br>Subject: <span style="color:black"> vtpm atlas contains no right IPS5 <br></span></div><br> <blockquote type="cite" class="clean_bq"><span><div style="word-wrap:break-word"><div></div><div>
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Dear Fieldtrippers,</div>
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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>
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<i>% load atlas</i></div>
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<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] = voxelcoords(atl.dim,
atl.transform);</i></div>
<div><i>atl.pos = [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 = find(strcmp(lower(atl.tissuelabel),
'IPS5'));</i></div>
<div>
<div><i>roi_mask = 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 = find(atl.pos(:, 1) > 0); </i></div>
<div><i>roi_mask(rightidx) = 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>
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