Flatmaps - NMT space #82
SjoerdMurris
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Hi!
We used NMT v2 template and ROIs to map to surface reconstructions (not
flatmaps) in this paper:
https://doi.org/10.1016/j.neuroimage.2021.118283
<https://doi.org/10.1016/j.neuroimage.2021.118283>
Please see Methods and e.g. Figures 4 and 5. The problem is that surface
reconstruction and visualization was done in BrainVoyager (commercial
package), although the same functionality now exists in NeuroElf package
that runs in MATLAB.
I can share intermediate and final files if you think it might be useful.
Cheers,
Igor
…--
Dr. Igor Kagan
Head of Decision and Awareness Group, German Primate Center (DPZ)
Kellnerweg 4, Goettingen 37077, Germany
http://www.dpz.eu/dag
On 12/4/2023 1:57 PM, 'SjoerdMurris' via NHP-MRI wrote:
Hi everyone,
I've been looking to plot flatmaps in monkey template space (NMT). But
perhaps someone here has already done so? If that's the case, it would
be great if someone could share or provide additional info on that. :-)
I have made flatmaps of D99 in the (somewhat distant) past before with
freesurfer, and flatmaps of individual monkeys.
So I can (and will) of course go ahead and share the maps here, once
I've made them. But again, do reach out if you've gone through this
process already!
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<p>Hi!</p>
<p>We used NMT v2 template and ROIs to map to surface
reconstructions (not flatmaps) in this paper: <a
class="anchor doi anchor-default"
href="https://doi.org/10.1016/j.neuroimage.2021.118283"
target="_blank" rel="noreferrer noopener"
aria-label="Persistent link using digital object identifier"
title="Persistent link using digital object identifier"
style="box-sizing: border-box; margin: 0px; padding: 0px; background-color: transparent; word-break: break-word; color: rgb(31, 31, 31); transition: color 0.3s ease 0s, border-bottom-color 0.3s ease 0s; text-decoration: none; display: inline-block; outline-width: 0px; font-family: ElsevierSans, Arial, Helvetica, Roboto, "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", STIXGeneral, "Cambria Math", "Arial Unicode MS", sans-serif; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal;"><span
class="anchor-text"
style="box-sizing: border-box; margin: 0px; padding: 0px; border-bottom: 2px solid rgb(235, 101, 0); transition: border-bottom-color 0.3s ease 0s;">https://doi.org/10.1016/j.neuroimage.2021.118283</span></a></p>
<p>Please see Methods and e.g. Figures 4 and 5. The problem is that
surface reconstruction and visualization was done in BrainVoyager
(commercial package), although the same functionality now exists
in NeuroElf package that runs in MATLAB. <br>
</p>
<p>I can share intermediate and final files if you think it might be
useful.</p>
<p>Cheers,<br>
Igor</p>
<pre class="moz-signature" cols="72">--
Dr. Igor Kagan
Head of Decision and Awareness Group, German Primate Center (DPZ)
Kellnerweg 4, Goettingen 37077, Germany
<a class="moz-txt-link-freetext" href="http://www.dpz.eu/dag">http://www.dpz.eu/dag</a></pre>
<p><br>
</p>
<p><br>
</p>
<p></p>
<div class="moz-cite-prefix">On 12/4/2023 1:57 PM, 'SjoerdMurris'
via NHP-MRI wrote:<br>
</div>
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<p dir="auto">Hi everyone,</p>
<p dir="auto">I've been looking to plot flatmaps in monkey
template space (NMT). But perhaps someone here has already done
so? If that's the case, it would be great if someone could share
or provide additional info on that. :-)</p>
<p dir="auto">I have made flatmaps of D99 in the (somewhat
distant) past before with freesurfer, and flatmaps of individual
monkeys.<br>
So I can (and will) of course go ahead and share the maps here,
once I've made them. But again, do reach out if you've gone
through this process already!</p>
<p
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Hi Igor, Thanks for your suggestion! I went through your paper before, which I think is great both in terms of both content and visualization. We do have some inflated surfaces of NMT generated through freesurfer tools (I'm a cheapskate when it comes to software packages), but I'm specifically looking for flatmaps. What do you think about the NeuroElf package in MATLAB, is it easy to use? Cheers, |
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Dear Sjoerd,
Thanks, and apologies for delayed response! No, I don't think NeuroElf can
do flatmaps - but yes, it is easy to use (object-oriented code) and easy to
integrate into other pipelines.
Cheers,
Igor
…On Fri, Dec 8, 2023 at 10:25 AM 'SjoerdMurris' via NHP-MRI < ***@***.***> wrote:
Hi Igor,
Thanks for your suggestion! I went through your paper before, which I
think is great both in terms of both content and visualization.
We do have some inflated surfaces of NMT generated through freesurfer
tools (I'm a cheapskate when it comes to software packages), but I'm
specifically looking for flatmaps. What do you think about the NeuroElf
package in MATLAB, is it easy to use?
Leaning towards using freesurfer tools for reconstruction and python-based
tools (PyCortex) for visualization purposes.
Cheers,
Sjoerd
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Hi everyone,
I've been looking to plot flatmaps in monkey template space (NMT). But perhaps someone here has already done so? If that's the case, it would be great if someone could share or provide additional info on that. :-)
I have made flatmaps of D99 in the (somewhat distant) past before with freesurfer, and flatmaps of individual monkeys.
So I can (and will) of course go ahead and share the maps here, once I've made them. But again, do reach out if you've gone through this process already!
Beta Was this translation helpful? Give feedback.
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