<div dir="ltr">Hi Tzvetan, Fieldtrippers,<div><br></div><div>see below the response I got from Liang Wang.</div><div><br></div><div><div style="font-size:12.800000190734863px"><i>I double-check the original files of the maximum probabilistic atlas in the volume-based space. As you said, it did not include left IPS5 areas. In our paper, we had pointed out that there was a difference between volume- and surface-based atlas, because the registration used between two space was totally different. We think the surface-based atlas may be more accurate, compare to the volume-based atlas. If you need to get left IPS5, I suggest to use the probability map for that region that you also can download from the web. This map provides you a probability value for each voxel being to that region. </i></div><div style="font-size:12.800000190734863px"><i><br></i></div><div style="font-size:12.800000190734863px"><i>Best,</i></div><div style="font-size:12.800000190734863px"><i>Liang</i></div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><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" target="_blank">www.anneurai.net</a> / @AnneEUrai</div></div></div></div></div>
<br><div class="gmail_quote">On 18 July 2017 at 10:12, Anne Urai <span dir="ltr"><<a href="mailto:anne.urai@gmail.com" target="_blank">anne.urai@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div id="m_-2618582950578579342bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Dear Liang,</div><div id="m_-2618582950578579342bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">cc Tzvetan, FieldTrip</div> <div><br></div>See the conversation below - Tzvetan has indicated that the volumetric representation is already missing IPS5. It would be great to try and redo the projection into volume space and play with the threshold to make sure that all regions are at least assigned to one voxel.<div><br></div><div>Best,<br><div><div><span class=""><br> <div id="m_-2618582950578579342bloop_sign_1500365087331336960" class="m_-2618582950578579342bloop_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" target="_blank">www.anneurai.net</a> / @AnneEUrai</div></div> </span><div class="m_-2618582950578579342airmail_ext_on" style="color:black"><br>From: <span style="color:black">Tzvetan Popov</span> <a href="mailto:tzvetan.popov@uni-konstanz.de" target="_blank"><tzvetan.popov@uni-konstanz.<wbr>de></a><br>Reply: <span style="color:black">FieldTrip discussion list</span> <a href="mailto:fieldtrip@science.ru.nl" target="_blank"><fieldtrip@science.ru.nl></a><br>Date: <span style="color:black">18 July 2017 at 09:28:28</span><br>To: <span style="color:black">FieldTrip discussion list</span> <a href="mailto:fieldtrip@science.ru.nl" target="_blank"><fieldtrip@science.ru.nl></a><br>Subject: <span style="color:black"> Re: [FieldTrip] vtpm atlas contains no right IPS5 <br></span></div><br> <blockquote type="cite" class="m_-2618582950578579342clean_bq"><span><div style="word-wrap:break-word"><div></div><div><div><div class="h5">
<div>Dear Anne,<br>
<blockquote type="cite">
<div>
<div id="m_-2618582950578579342bloop_customfont" style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;margin:0px">
<pre style="white-space:pre-wrap"></pre>
<div id="m_-2618582950578579342bloop_customfont" style="white-space:normal;margin:0px">
<div style="font-family:Helvetica,Arial;font-size:13px">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</div>
</div>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div>
<div id="m_-2618582950578579342bloop_customfont" style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;margin:0px">
<pre style="white-space:pre-wrap"></pre>
<div id="m_-2618582950578579342bloop_customfont" style="white-space:normal;margin:0px">
<div style="font-family:Helvetica,Arial;font-size:13px">Do you know by
any chance which author provided the mat file</div>
</div>
</div>
</div>
</blockquote>
I have created the mat file working from the nifti files. I don’t
have the code anymore but it wasn’t too difficult. Yet, this code
wouldn’t help since the ROI isn’t in the nifti files to begin with.
I had exchange RE: missing ROI with Michael Arcaro back then. Here
is what he wrote:</div>
<div><br></div>
<div>"As you said, ROI 23 does not appear to be in the volume lh
map.<br>
It’s there in the surface max prob map for the lh. I know Liang
generated a separate probability map using nonlinear volumetric
alignment, which was a little bit worse in quality than the surface
map. It’s possible you’re using that map. I thought we sent you the
volume projection of the surface max probability map though. It’s
possible that the small area of ROI3 in the surface max probability
map did not survive the projection back into volume space (since
there is interpolation in the projection). I’ll double check with
Liang and Ryan and see if they remember any issues with ROI23. It
might be better to use the individual probability map for ROI 23
and use a more liberal threshold."</div>
<div><br></div>
<div>So it seems that Liang could indeed provide some more info on
whether and how to use a more liberal threshold to get the ROI back
into the volumetric representation?</div>
<div><br></div>
<div>Best</div>
<div>tzvetan</div>
<div><br></div></div></div>
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