----- Forwarded message from Stefan Schlager <[email protected]> -----
Date: Thu, 14 Mar 2013 10:35:58 -0400
From: Stefan Schlager <[email protected]>
Reply-To: Stefan Schlager <[email protected]>
Subject: Re: Software for landmarks
To: [email protected]
Hi William,
If you are dealing with large meshes, you can usually reduce the
surfaces, e.g. by quadric mesh collapse decimation, you can use meshlab
for example (batch processing makes things quick).
I usually place landmarks, then, in the free landmark editor landmark or
in meshlab.
My R-package Morpho (https://sourceforge.net/projects/morpho-rpackage/)
allows a semi-automatic patch-placement procedure based on manually
placed landmarks/ curves (if you are interested, I can write
documentation for this function - it is not yet officially
documented...and a bit nerdy). There are also two other packages on my
sourceforge page, enabling providing mesh processing tools: Rvcg
introduces some meshlab functionalities for R, while mesheR has some
surface-matching and point selection features. If you want to use those,
drop me a line.
For sliding, you can also use Morpho - hereby large meshes are no
problem, as they are not loaded into your R-workspace - the
semi-landmarks are re-projected onto those meshes externally after each
iteration.
Best regards
Stefan
Stefan Schlager M.A.
Anthropologie
Medizinische Fakultät der der Albert Ludwigs- Universität Freiburg
Hebelstr. 29
79104 Freiburg
Anthropology
Faculty of Medicine, Albert-Ludwigs-University Freiburg
Hebelstr. 29
D- 79104 Freiburg
phone +49 (0)761 203-5522
fax +49 (0)761 203-6898
On 14/03/13 04:43, [email protected] wrote:
> ----- Forwarded message from William Ary <[email protected]> -----
>
> Date: Wed, 13 Mar 2013 17:25:31 -0400
> From: William Ary <[email protected]>
> Reply-To: William Ary <[email protected]>
> Subject: Software for landmarks
> To: [email protected]
>
> Hello, everyone-
>
> My lab is using segmented high-resolution CT images to generate models
> for geometric morphometrics. I am having problems doing the following:
>
> 1. Finding homologous landmarks for smooth bones that have no
> intersections with other bones. This forces us to use less repeatable
> things like ridges and prominences that are harder to place landmarks
> on in a consistent manner. I plan to use a sliding semilandmark method
> to solve this problem, possibly a 3-D version as I have heard that the
> Geomorph package in R handles 3D semilandmarks. Other packages like
> SPHARM, MorphoJ, Morphologika etc. are in the running if they can
> solve my landmark issue.
>
> 2. Picking a software for placing landmarks that works with our large
> high-resolution models with millions of elements. I have sampled the
> vast array of programs to some degree, having tried Paraview, Meshlab,
> MiniMagics, and our segmentation software, Analyze. I have encountered
> problems with all of them as follows:
>
> Paraview- Doesn't record points, cannot find way to place multiple
> points, doesn't record Cartesian 3-space coordinates.
> Meshlab- Looked great but bogs down or crashes when placing points,
> likely due to model complexity
> MiniMagics- Could not figure out how to place multiple landmarks/model
> size issues. Investigating if MIMICS is better.
> Analyze- Points disappear on the topology of the model and are hard to
> see once the model is moved.
>
> After all this, I welcome any suggestions you may have on which
> programs allow picking landmarks/semilandmarks on high resolution
> models and how to generate landmarks on our smooth bones. We are
> hoping there is an alternative to coarsening our models. I would be
> especially grateful to know how to go about placing a series of
> sliding semilandmarks. I have read some papers on this, but suggested
> reading is always appreciated!
>
> Many thanks!
>
> Will Ary
> Master's candidate
> San Diego State University
> [email protected]
>
> ----- End forwarded message -----
>
----- End forwarded message -----
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