mri_synthmorph-apply

NAME
        mri_synthmorph-apply - apply an existing SynthMorph transform

SYNOPSIS
        mri_synthmorph apply [options] trans image output [image output ...]

DESCRIPTION
        Apply a spatial transform trans estimated by SynthMorph to a 3D image
        and write the result to output. You can pass any number of image-output
        pairs to be processed in the same way.

        The following options identically affect all input-output pairs.

        -H
                Update the voxel-to-world matrix of output instead of
                resampling. For matrix transforms only. Not all software and
                file formats support headers with shear from affine
                registration.

        -m method
                Interpolation method (linear, nearest). Defaults to linear.
                Choose linear for images and nearest for label (segmentation)
                maps.

        -t type
                Output data type (uint8, uint16, int16, int32, float32).
                Defaults to float32. Casting to a type other than float32 after
                linear interpolation may result in information loss.

        -f fill
                Extrapolation fill value for areas outside the field-of-view of
                image. Defaults to 0.

        -h
                Print this help text and exit.

EXAMPLES
        Apply an affine transform to an image:
                # mri_synthmorph apply affine.lta image.nii out.nii.gz

        Apply a warp to an image, saving the output in floating-point format:
                # mri_synthmorph apply -t float32 warp.nii image.nii out.nii

        Apply the same transform to two images:
                # mri_synthmorph app warp.mgz im_1.mgz out_1.mgz im_2.mgz
                out_2.mgz

        Transform a label map:
                # mri_synthmorph apply -m nearest warp.nii labels.nii out.nii