antsApplyTransforms

[marivas-MRI]

Hi,

I have two images (A.nii, B.nii). After perform SyN registration from A.nii to B.nii, I obtained the C0GenericAffine.mat, C1InverseWarp.nii.gz and the C1Warp.nii.gz files.

Now my goal is to apply the registration fields obtained in registration A.nii ---> B.nii to the A.nii image. For that purpose I am trying to use the antsApplyTransforms using this command:

antsApplyTransforms ('B.nii', 'A.nii', transformlist = "C0GenericAffine.mat", interpolator = 'nearestNeighbor', imagetype = 0, whichtoinvert = FALSE, compose = NA, verbose = FALSE)

and the output is

[1] 1

I am very new using ANTsR tools, can anyone suggest to me the correct command to apply the deformation fields to the A.nii image??

Thanks for your help.

Best regards,

[stnava]

see ?antsApplyTransforms

[marivas-MRI]

Before asking I have tried to follow the instructions and again I have not been able to do it correctly. Could you help me please?

Thank you and excuse me for this kind of questions.

Best,

[ntustison]

If you type ?antsApplyTransforms, you'll see an example that you should try to reproduce before asking about your specific example.

[ptsii]

Here's what I do:

First the registration:

ImageA_into_ImageB_reg<-antsRegistration(ImageB, ImageA, typeofTransform = "SyNRA")

First, note that the resulting object: ImageA_into_ImageB_reg itself CONTAINS ImageA transformed into ImageB already. If you enter the name of this object by itself on R's commandline, you get something like:

> ImageA_into_ImageB_reg

$warpedmovout
antsImage
  Pixel Type          : float 
  Components Per Pixel: 1 
  Dimensions          : 218x209x255 
  Voxel Spacing       : 0.75x0.75x0.75 
  Origin              : 6.75 6.75 -3.75 
  Direction           : -1 0 0 0 -1 0 0 0 1 


$warpedfixout
antsImage
  Pixel Type          : float 
  Components Per Pixel: 1 
  Dimensions          : 218x209x255 
  Voxel Spacing       : 0.75x0.75x0.75 
  Origin              : 6.75 6.75 -3.75 
  Direction           : -1 0 0 0 -1 0 0 0 1 


$fwdtransforms
[1] "/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpV5JKx3/file8134589d25581Warp.nii.gz"      
[2] "/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpV5JKx3/file8134589d25580GenericAffine.mat"

$invtransforms
[1] "/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpV5JKx3/file8134589d25580GenericAffine.mat" 
[2] "/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpV5JKx3/file8134589d25581InverseWarp.nii.gz"

$prev_transforms
character(0)

In other words, ImageA_into_ImageB_reg$warpedmovout is (in this case) ImageA warped into ImageB. You can check this by doing:

plot(ImageA_into_ImageB_reg$warpedmovout)

(Similarly ImageA_into_ImageB_reg$warpedfixout is ImageB warped into ImageA)

However, these are created using (I believe) linear interpolation. If you want to use a different kind of interpretation, you'd use antsApplyTransforms, and specify a particular type of interpolation. For example:

ImageA_in_ImageB_nearestNeighbor_interpolation_image<-antsApplyTransforms(ImageB, ImageA, transformlist = ImageA_into_ImageB_reg$fwdtransforms, interpolator = "nearestNeighbor")
This would apply nearest-neighbor interpolation to the transform.

I believe this is correct...

-Tom