Re: [MORPHMET] Curve sliding semilandmarks

[Stefan Schlager]

Be careful to dampen the displacement along the tangents, as there is no
surface to project the landmarks back to. Using Morpho, you can control
this using the parameter "stepsize".
Best
Stefan

On 06/12/16 19:21, Lawrence Fatica wrote:
>
> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I
> used IDAV Landmark to place four curves of five semilandmarks each (as
> well as several fixed landmarks) along the major contours of the
> pelvis. I plan on doing the analysis in R, but I am unsure what my
> options are for semilandmarks sliding along curves. I am particularly
> concerned that the semilandmarks will slide along their tangents and
> off the bone when using sliding protocols that do not include the 3D
> mesh itself.
>
> Is this something I should be worried about? Has anyone else had
> success using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google
> Groups "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to morphmet+unsubscr...@morphometrics.org
> .


-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


signature.asc
Description: OpenPGP digital signature

Re: [MORPHMET] Curve sliding semilandmarks

[Emma Sherratt]

Dear Lawrence,

You can use geomorph's gpagen function for sliding semilandmarks during
Procrustes superimposition, by minimising bending energy or by minimising
Procrustes distance.

I would say that it is better to sample the curve in IDAV Landmark
Editorwith many semilandmarks, in order to avoid as many issues of
smoothing the curve of interest. Also, if you link two or more curves
together in IDAV Landmark Editor, then first use digit.curves function in
geomorph to resample the semilandmarks of those curves (since IDAV Landmark
Editor does not consider two curves sharing 1 landmark as linked and places
equally distant semis on each curve separately).

Details of geomorph below in my signature, including the extensive help
guide.

Emma

~~~

Emma Sherratt, PhD.


Postdoctoral Researcher in the Keogh Lab

Division of Evolution, Ecology & Genetics
Research School of Biology
116 Daley Road
The Australian National University
Acton, ACT  2601
AUSTRALIA

email: emma.sherr...@gmail.com
office tel: +61 2612 54943
mob: +61 4234 19966
Twitter: @DrEmSherratt 
co-author of geomorph R package: Software website
 | CRAN website
 | googlegroups


Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians




On 7 December 2016 at 05:21, Lawrence Fatica 
wrote:

> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I used
> IDAV Landmark to place four curves of five semilandmarks each (as well as
> several fixed landmarks) along the major contours of the pelvis. I plan on
> doing the analysis in R, but I am unsure what my options are for
> semilandmarks sliding along curves. I am particularly concerned that the
> semilandmarks will slide along their tangents and off the bone when using
> sliding protocols that do not include the 3D mesh itself.
>
> Is this something I should be worried about? Has anyone else had success
> using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

Re: [MORPHMET] Curve sliding semilandmarks

[Thomas O'Mahoney]

Dear Lawrence,
Stefan Schlager's excellent Morpho package for R has the option to slide
semilandmarks without the mesh. I have had some success with this myself,
but you can of course include your mesh with these protocols in either
Morpho or Geomorph (written by Dean Adams et al.).
Best,
Tom

On 6 December 2016 at 18:21, Lawrence Fatica 
wrote:

> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I used
> IDAV Landmark to place four curves of five semilandmarks each (as well as
> several fixed landmarks) along the major contours of the pelvis. I plan on
> doing the analysis in R, but I am unsure what my options are for
> semilandmarks sliding along curves. I am particularly concerned that the
> semilandmarks will slide along their tangents and off the bone when using
> sliding protocols that do not include the 3D mesh itself.
>
> Is this something I should be worried about? Has anyone else had success
> using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

[MORPHMET] Curve sliding semilandmarks

[Lawrence Fatica]

 

Hi all,

I am working on a project examining shape variation in the pelvis. I used 
IDAV Landmark to place four curves of five semilandmarks each (as well as 
several fixed landmarks) along the major contours of the pelvis. I plan on 
doing the analysis in R, but I am unsure what my options are for 
semilandmarks sliding along curves. I am particularly concerned that the 
semilandmarks will slide along their tangents and off the bone when using 
sliding protocols that do not include the 3D mesh itself.

Is this something I should be worried about? Has anyone else had success 
using sliding semilandmarks along curves?


Thanks in advance for any insight,

Lawrence

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.