landmark registration

[Ruben Portugues]

Hi Greg,

 

I am sorry to bother you with something trivial, but I am trying to get the fit_affine_xform_landmarks to work in CMTK.  I am entering the following command

 

fit_affine_xform_landmarks --rigid source.landmarks target.landmarks output.xform

 

My source.landmarks file is

 

<namedpointset version="1.0">

<pointworld set="true" name="point 1" x="433.0" y="95.0" z="51.0"/>

<pointworld set="true" name="point 2" x="310.0" y="404.0" z="93.0"/>

<pointworld set="true" name="point 3" x="262.0" y="302.0" z="119.0"/>

</namedpointset>

 

And I have an analogous file as the target (testing it with 3 points and a rigid transformation).  The command just runs (for ever).

I also tried using the landmarks plugin for Fiji, but I could not see how to save the xform folder so that I could later apply it to more stacks.

 

Thanks for any help you can provide.

 

Best,

Ruben

[Greg Jefferis]

Dear Ruben,

I'm sorry to see that this question never got answered here. I imagine you must be sorted by now. For reference.

1. The landmarks you show below are not in the CMTK format.

2. CMTK would like its own format, which you can export from the the Fiji http://imagej.net/Name_Landmarks_and_Register plugin (Export to IGS button in older versions, Export to CMTK now).

3. You can also use nat to convert between different landmarks formats

library(nat)
x=read.landmarks('myfijiformatpoints')
write.landmarks(x, 'mylandmarks.cmtk', format='cmtk')

See http://jefferis.github.io/nat/reference/read.landmarks.html

Best,

Greg.