Corresponding Points

[Amirhossein Jalalzadeh]

Hi all, 

First of all, apologize for my multiple question! im new in ELASTIX 

I find out from manual pdf that corresponding points can calculate by (TransformParameters.txt)

Here i engaged to 4 problems:

1- How i can use prepared Landmarks before start registration?? in the other words, I intent to use these points in registration process for increasing accuracy. Since, in manual pdf mentioned we should import them in TRANSFORMIX, which actually it is after registration and doesn't affect the registration accuracy. Am i wrong? 

2- according to previous question, what is correct format  and structure for describe Landmarks as txt file?? 

3- my Landmarks defined in 'mm' coordinate. 

can I use them or I have to convert them to Voxel coordinate? 

4- manual pdf in TRANSFORMIX section, define corresponding points should save as txt format. In the first line we should determine <index or points>

The problem is what is world coordinate? 

Is it calculated by images origins or measure  distance from [ 0 0 0]??? 

Best regards 

[Viktor van der Valk]

Hi Amirhossein,

In elastix you can do two things with point sets:

1. Use two corresponding point sets to aid registration of two images. (This could increase the accurary of your registration and is done with elastix.)
2. Transform a pointset with a transformparameters.txt file, this is done with transformix.

The correct structure of a pointset.txt file can be found in the manual:

"The inputPoints.txt file should have the following structure:

<index, point>

<number of points>

point1 x point1 y [point1 z] 

point2 x point2 y [point2 z] 

The first line indicates whether the points are given as “indices” (of the fixed image), or as “points” (in physical coordinates). The second line stores the number of points that will be specified. After that the point data is given."

So "indices" with depend on the image origin and "points" is for world coordinates.

For examples of pointsets registration and transformation in python (itkelastix) you could check out the example notebooks 5 and 9.

Best,
Viktor

Op dinsdag 4 mei 2021 om 21:18:46 UTC+2 schreef amirh...@gmail.com:

[Amirhossein Jalalzadeh]

Thanks a lot for your reply, Victor

As you said, the Points file structure to aid registration is same as used in TRANSFORMIX.

I wonder where should I define the points file in command line. According the below picture, there is no command for this, even in Optional extra commands. Would you please explain this to me?

Appreciate your help

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[Viktor van der Valk]

Hi Amirhossein,

That's interesting, it should have been listed there.

However you can find it in the manual in the ''6.1.7 Corresponding points: help the registration" section:

"elastix ... -fp fixedPointSet.txt -mp movingPointSet.txt"

Please read the section, since it contains more info on which metrics to use when using pointsets to aid your registration.

Best,
Viktor

Op woensdag 5 mei 2021 om 17:36:08 UTC+2 schreef amirh...@gmail.com:

[Amirhossein Jalalzadeh]

Thank you so much for your time and great help🙏🏻🙏🏻🙏🏻

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[Niels Dekker]

Hi Amir Hossein,

Can you please have a look at the following pull request?

  "ENH: Help should mention optional point set arguments"

  https://github.com/SuperElastix/elastix/pull/462

It should address your comment regarding `elastix --help`

Kind regards, Niels