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