[MORPHMET] Re: Computing a species average from a set of landmarks

[Grace Capshaw]

I received a helpful reply from Murat Maga that I wanted to share here for 
anyone having the same issue (I haven't tried yet, but looks promising!)



I am not sure how IDAV does it, but you can use R/Morpho to achieve an 
> average in a manner like this: You need to read your all your landmarks, do 
> a Procrustes fit without scaling, then provide a sample as reference. This 
> sample is typically the sample that is closest the Procrustes mean .  
>
>  
>
>  
>
> gpa=procSym(LM, scale = FALSE, CSinit = FALSE)
>
> #LM is the array of all your landmarks 
>
>  
>
> sample.mean = tps3d (refmat = reference.lm, tarmat = gpa$mshape, x =  
> reference.mesh)
>
> #reference.mesh is the ply file of the sample closest to the Procrustes 
> mean
>
> #reference.lm is landmark set associated with the mesh above. 
>
>  
>
> Then you can write your sample mean with command
>
> Rvcg::vcgPlyWrite(mesh = sample.mean, filename = …)
>
>
>
 

On Monday, November 12, 2018 at 4:00:17 PM UTC-5, Grace Capshaw wrote:
>
>
> Hi all,
>
> I am currently using Landmark IDAV to place landmarks onto .ply mesh 
> files, but when I try to compute a species average from several meshes the 
> software crashes. This happens even when I reduce the number of mesh files 
> to be averaged, and when I use the "Low Resolution" output option. Has 
> anyone run into this issue (and ideally, figured out how to fix it)? If 
> not, can anyone recommend a (free) software or R package that can compute a 
> species average from a set of landmarks?
>
> Thanks very much for your help!
>
> Best,
> Grace
>

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[MORPHMET] Computing a species average from a set of landmarks

[Grace Capshaw]

Hi all,

I am currently using Landmark IDAV to place landmarks onto .ply mesh files, 
but when I try to compute a species average from several meshes the 
software crashes. This happens even when I reduce the number of mesh files 
to be averaged, and when I use the "Low Resolution" output option. Has 
anyone run into this issue (and ideally, figured out how to fix it)? If 
not, can anyone recommend a (free) software or R package that can compute a 
species average from a set of landmarks?

Thanks very much for your help!

Best,
Grace

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[MORPHMET] Re: Looking for software to place landmarks on 3d data

[Grace Capshaw]

Thank you Terrie, I will look into those!

Best,
Grace
 

On Tuesday, May 9, 2017 at 7:42:38 AM UTC-4, terrielsimmons wrote:
>
> Hi Grace,
>
> You can use 3D Slicer or Meshlab to place points on 3D models--both are 
> free.
>
> Terrie
>
> On Tuesday, May 9, 2017 at 7:26:04 AM UTC-4, Grace Capshaw wrote:
>>
>> Hi all, 
>>
>> I am attempting to analyze 3D data reconstructed from CT scans (.ply 
>> files). Can anyone recommend a program to help me place landmarks on these 
>> data? 
>>
>> I tried to download Landmark Editor, but it seems like the download links 
>> on the IDAV website are no longer functioning. I found an archived version 
>> of the software online, but it constantly crashes when I import my data. Is 
>> this the only free software that can be used to apply landmark points to 3D 
>> data? 
>>
>> Thanks in advance! 
>> - Grace
>
>

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Re: [MORPHMET] Looking for software to place landmarks on 3d data

[Grace Capshaw]

Thanks so much, I'll give it a try!

On Tuesday, May 9, 2017 at 7:43:50 AM UTC-4, Vera Moitinho wrote:
>
> Dear Grace,
>
> I'm sending you the link to download Landmark software + manual 
> .
> This version of the software used to work well.
> Hope this helps!
>
> Best,
> Vera
>
>
> On Tue, May 2, 2017 at 6:53 PM, Grace C.  
> wrote:
>
>> Hi all,
>>
>> I am attempting to analyze 3D data reconstructed from CT scans (.ply 
>> files). Can anyone recommend a program to help me place landmarks on these 
>> data?
>>
>> I tried to download Landmark Editor, but it seems like the download links 
>> on the IDAV website are no longer functioning. I found an archived version 
>> of the software online, but it constantly crashes when I import my data. Is 
>> this the only free software that can be used to apply landmark points to 3D 
>> data?
>>
>> Thanks in advance!
>> - Grace
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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>
>

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