Transforming to the Jacobian Domain

1

I need to understand what is tx in ANTspy
Can the TX be the MNI152_T1_1mm_brain.nii.gz file?
Using flirt, I aligned the T1w together by setting one T1w image as the reference and aligned the rest on it.
The ref T1w was transformed to MNI152 first before using it. Now I want to use ants to transform to the Jacobian domain, So what’s the correct way to use the below function to transform the T1w images to jacobian?

def create_jacobian_determinant_image(domain_image, tx, do_log=False, geom=False):
    """
    Compute the jacobian determinant from a transformation file
   
    ANTsR function: `createJacobianDeterminantImage`

    Arguments
    ---------
    domain_image : ANTsImage
        image that defines transformation domain
    
    tx : string
        deformation transformation file name
    
    do_log : boolean
        return the log jacobian
    
    geom : bolean
        use the geometric jacobian calculation (boolean)
    
    Returns
    -------
    ANTsImage

    Example
    -------
    >>> import ants
    >>> fi = ants.image_read( ants.get_ants_data('r16'))
    >>> mi = ants.image_read( ants.get_ants_data('r64'))
    >>> fi = ants.resample_image(fi,(128,128),1,0)
2

Hi @Yasmine,

tx refers to the transformation of interest, as produced by ANTs. The jacobian determinant is a property related to the transform, and is not a space to align images to.

Best,
Steven

3

So MNI152 can be the transformation of interest, for example?

4

The transformation to MNI, yes. But for this to work you will probably have to use ANTs to register, I doubt it will accept FLIRT files.

1 Like