RE: [MORPHMET] Help with .tif files

2017-02-03 Thread Murat Maga
Alexa,
I believe Slicer reads tif files as a vector (RGB) image. You need to use 
“convert vector to scalar” module to convert it a grayscale volume. Next, you 
need to use the “editor” module to create a labelmap (binary) image that will 
be the basis for the isosurfacing operation to make a 3D model. Once you 
prepare your label map to your satisfaction, you can use the “model maker” 
module to turn it into a polygonial model, which you can save as ply, stl or 
vtk formats.

I suggest you go through their tutorials in detail on their website
https://www.slicer.org/wiki/Documentation/4.6/Training

this youtube video shows the process for an older version of slicer. Menus now 
look different, but the steps are identical
https://www.youtube.com/watch?v=og3t1i9gSG0



From: Alexa Martinez-Melo [mailto:a.mtz.m...@gmail.com]
Sent: Friday, February 03, 2017 9:22 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Help with .tif files

Hello.
I'm working with on ontogeny of irregular echinoids.
I'm able to get .tif files from CT scan, but I need 3D models in .ply format; 
when I try to get them in 3DSlicer, the software shuts down.

Could you help me with that? I need some advice, so I could start my analysis.

Have a great weekend, everyone!

--
Dra. Alejandra Martínez Melo
Departamento de Paleontología
Instituto de Geología
Universidad Nacional Autónoma de México.
(55) 5622-4283 ext. 211
--
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[MORPHMET] Help with .tif files

2017-02-03 Thread Alexa Martinez-Melo
Hello.

I'm working with on ontogeny of irregular echinoids.

I'm able to get .tif files from CT scan, but I need 3D models in .ply
format; when I try to get them in 3DSlicer, the software shuts down.



Could you help me with that? I need some advice, so I could start my
analysis.


Have a great weekend, everyone!

-- 
Dra. Alejandra Martínez Melo
Departamento de Paleontología
Instituto de Geología
Universidad Nacional Autónoma de México.
(55) 5622-4283 ext. 211

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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Re: [MORPHMET] Landmark Editor - download problem

2017-02-03 Thread Vera Moitinho
Dear Terry,

I can´t attach an exe to my email. I'm sending you the software via
WeTransfer.
It used to work in my computer. Hope this helps.

Best,
Vera

Vera Moitinho de Almeida
Postdoctoral Researcher
Quantitative Archaeology Lab (LAQU)
Universitat Autònoma de Barcelona
https://www.researchgate.net/profile/Vera_Moitinho


On Tue, Jan 31, 2017 at 8:59 PM, Terry Ritzman  wrote:

> Hi all,
>
> I am having trouble downloading the .exe file for Landmark Editor from the
> website for the
> software.  I have tried from a number of computers and have asked
> colleagues to try on their machines, to no avail. Does anyone have a fix
> and/or an alternative for downloading the program?
>
> Thanks,
>
> Terry Ritzman
> Postdoctoral Research Associate
> Department of Neuroscience
> Washington University School of Medicine
> terryritzman.com
> primate-radiograph.com
>
>
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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RE: [MORPHMET] Procrustes ANOVA for FA Analysis

2017-02-03 Thread imronnawawi


Sent from Mail for Windows 10

From: M. Viviana Toro Ibacache
Sent: Friday, 3 February 2017 9:27 PM
To: Kate Rusk
Cc: MORPHMET
Subject: Re: [MORPHMET] Procrustes ANOVA for FA Analysis

Hi Kate,

If I understood correctly, I am not sure that you can do a Procrustes 
ANOVA-based FA test on a list of individuals where only few of them have been 
digitized a second time. If this is the case, then I would suggest this 
approach (might be other ones using what you already have but this is fast and 
works for me):

- have a separate landmark file that contains only the specimens you repeated 
(5 landmarks sets + 5 repeatded landmark sets = 10 landmark sets), whose names 
end on "-rep1" and "-rep2" or something alike but with the same amount of 
characters.
- create a classifier (eg "repeat) using the last characters of the name (in my 
example, first character would be -5 and the last, -1). Remember you have to 
create an "individual" classifier that covers all the remainig characters.
- run the procrustes ANOVA on this 10-individuals landmark set using as error 
term the "repeat" classifier. This way you will be able to quantify variation 
due to repeated landmarking against variation due to individual*side.

I hope this helps,
Viviana

2017-01-30 20:56 GMT+01:00 Kate Rusk :
Hello everyone,

I am a bit confused about how to properly import and classify data for a 
Procrustes ANOVA in MorphoJ. Here is some more information about my data:

15 3D landmarks on human faces (object symmetry)
479 individuals
15 landmarks from 5 individuals digitized a second time
Sex and age as additional main effects

I realize I need to include a classifier that indicates a repeat (to be added 
as an Error classifier), but I am unsure how to import these data. So far, I 
have imported 1) the original data text file which includes the identifier and 
the XYZ coordinates for the original 15 landmarks and 2) a classifier text file 
which includes sex and age as covariates. I have separate XYZ coordinates for 
the repeat landmarks, but I don't know how these should be imported to 
implement the "repeat" classifier.

Any assistance you could provide would be greatly appreciated!

Thanks very much,
Kate

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-- 

Viviana Toro-Ibacache DDS MSc PhD
Profesora Asistente (Assistant Professor)
Centro de Análisis Cuantitativo en Antropología Dental (CA2)
Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
Facultad de Odontología Universidad de Chile

Dirección:  Sergio Livingstone Pohlhammer 943
(address)   Independencia, Región Metropolitana
                 Chile
Email:        mtoroibaca...@odontologia.uchile.cl
Web:         www.researchgate.net/profile/Viviana_Toro_Ibacache/
                 www.cienciaymemoria.cl/staff.html
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Re: [MORPHMET] Procrustes ANOVA for FA Analysis

2017-02-03 Thread M. Viviana Toro Ibacache
Hi Kate,

If I understood correctly, I am not sure that you can do a Procrustes
ANOVA-based FA test on a list of individuals where only few of them have
been digitized a second time. If this is the case, then I would suggest
this approach (might be other ones using what you already have but this is
fast and works for me):

- have a separate landmark file that contains only the specimens you
repeated (5 landmarks sets + 5 repeatded landmark sets = 10 landmark sets),
whose names end on "-rep1" and "-rep2" or something alike but with the same
amount of characters.
- create a classifier (eg "repeat) using the last characters of the name
(in my example, first character would be -5 and the last, -1). Remember you
have to create an "individual" classifier that covers all the remainig
characters.
- run the procrustes ANOVA on this 10-individuals landmark set using as
error term the "repeat" classifier. This way you will be able to quantify
variation due to repeated landmarking against variation due to
individual*side.

I hope this helps,
Viviana

2017-01-30 20:56 GMT+01:00 Kate Rusk :

> Hello everyone,
>
> I am a bit confused about how to properly import and classify data for a
> Procrustes ANOVA in MorphoJ. Here is some more information about my data:
>
> 15 3D landmarks on human faces (object symmetry)
> 479 individuals
> 15 landmarks from 5 individuals digitized a second time
> Sex and age as additional main effects
>
> I realize I need to include a classifier that indicates a repeat (to be
> added as an Error classifier), but I am unsure how to import these data. So
> far, I have imported 1) the original data text file which includes the
> identifier and the XYZ coordinates for the original 15 landmarks and 2) a
> classifier text file which includes sex and age as covariates. I have
> separate XYZ coordinates for the repeat landmarks, but I don't know how
> these should be imported to implement the "repeat" classifier.
>
> Any assistance you could provide would be greatly appreciated!
>
> Thanks very much,
> Kate
>
> --
> 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.
>



-- 

*Viviana Toro-Ibacache DDS MSc PhD*
Profesora Asistente *(Assistant Professor)*
Centro de Análisis Cuantitativo en Antropología Dental (CA2)
Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
Facultad de Odontología Universidad de Chile

Dirección:  Sergio Livingstone Pohlhammer 943
*(address)*   Independencia, Región Metropolitana
 Chile
Email:mtoroibaca...@odontologia.uchile.cl
Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/
 www.cienciaymemoria.cl/staff.html

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