Dimensionality / components of Nonlinear Warp Images

[nicolatoschi]

Dear Developers,

a "hopefully" quick question about the format in whcih nonlinear warps are outputted by ANTs.

I was expecting each warp image to have dimensions Nx Ny Nz 3, where the first three are teh size of fixed image and the fourth dimension would be the components of the local warp vector. Instead, the warp images are scalar images.

Could you please explain this format and, if possible, guide me in extracting the warp components?

Thank you in advance,

Nicola Toschi

[ntustison]

Self-contained 2-D example which you should be able to extrapolate to 3-D:

Python 3.7.6 (default, Jan  8 2020, 13:42:34) 
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ants
>>> r16 = ants.image_read(ants.get_ants_data("r16"))
>>> r64 = ants.image_read(ants.get_ants_data("r64"))
>>> reg = ants.registration(r16, r64, type_of_transform="antsRegistrationSyNQuick[so]")
>>> displacement_field = ants.image_read(reg['fwdtransforms'][0])
>>> displacement_field.shape
(256, 256)
>>> displacement_field
ANTsImage
     Pixel Type : float (float32)
     Components : 2
     Dimensions : (256, 256)
     Spacing    : (1.0, 1.0)
     Origin     : (0.0, 0.0)
     Direction  : [1. 0. 0. 1.]

>>> displacement_field_components = ants.split_channels(displacement_field)
>>> displacement_field_components
[ANTsImage
     Pixel Type : float (float32)
     Components : 1
     Dimensions : (256, 256)
     Spacing    : (1.0, 1.0)
     Origin     : (0.0, 0.0)
     Direction  : [1. 0. 0. 1.]
, ANTsImage
     Pixel Type : float (float32)
     Components : 1
     Dimensions : (256, 256)
     Spacing    : (1.0, 1.0)
     Origin     : (0.0, 0.0)
     Direction  : [1. 0. 0. 1.]
]
>>> 

[nicolatoschi]

Thank you so much.

At the moment I am simply working with the executables, i.e. with the .nii.gz Warp and Inversewarp images produced by antsRegistration.

Is there a bash executable equivalent to ants.split_channels in your python script?

Thank you again,

Nicola

On 3/7/2022 1:05 AM, Nick Tustison wrote:

Self-contained 2-D example which you should be able to extrapolate to 3-D:

|Python 3.7.6 (default, Jan 8 2020, 13:42:34) [Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import ants >>> r16 = ants.image_read(ants.get_ants_data("r16")) >>> r64 = ants.image_read(ants.get_ants_data("r64")) >>> reg = ants.registration(r16, r64, type_of_transform="antsRegistrationSyNQuick[so]") >>> displacement_field = ants.image_read(reg['fwdtransforms'][0]) >>> displacement_field.shape (256, 256) >>> displacement_field ANTsImage Pixel Type : float (float32) Components : 2 Dimensions : (256, 256) Spacing : (1.0, 1.0) Origin : (0.0, 0.0) Direction : [1. 0. 0. 1.] >>> displacement_field_components = ants.split_channels(displacement_field) >>> displacement_field_components [ANTsImage Pixel Type : float (float32) Components : 1 Dimensions : (256, 256) Spacing : (1.0, 1.0) Origin : (0.0, 0.0) Direction : [1. 0. 0. 1.] , ANTsImage Pixel Type : float (float32) Components : 1 Dimensions : (256, 256) Spacing : (1.0, 1.0) Origin : (0.0, 0.0) Direction : [1. 0. 0. 1.] ] >>> |

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[ntustison]

My mistake---been doing too much in ANTsPy and I failed to see the usage here. Note that this particular format/usage of the displacement fields completely stems from ITK.

But, yes, see ConvertImage (specifically option 10):

% ConvertImage
Usage: ConvertImage imageDimension inputImage outputImage <pixelType>
pixelType:  0 -> float (default)
            1 -> unsigned char
            2 -> unsigned short
            3 -> unsigned int
            4 -> unsigned long
            5 -> char
            6 -> short
            7 -> int
            8 -> long
            9 -> component images to a float vector image
           10 -> vector image to component images
           11 -> time-varying velocity field image to component images (ImageDimension is the dimensionality of the displacement vector)
           12 -> float vector image

[nicolatoschi]

Work perfectly, thank you!

nicola

On 3/7/2022 1:13 AM, Nick Tustison wrote:

My mistake---been doing too much in ANTsPy and I failed to see the usage here. Note that this particular format/usage of the displacement fields completely stems from ITK.

But, yes, see |ConvertImage| (specifically option 10):

|% ConvertImage Usage: ConvertImage imageDimension inputImage outputImage pixelType: 0 -> float (default) 1 -> unsigned char 2 -> unsigned short 3 -> unsigned int 4 -> unsigned long 5 -> char 6 -> short 7 -> int 8 -> long 9 -> component images to a float vector image 10 -> vector image to component images 11 -> time-varying velocity field image to component images (ImageDimension is the dimensionality of the displacement vector) 12 -> float vector image |

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