.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH WARPTENSORIMAGEMULTITRANSFORM "1" "September 2017" "WarpTensorImageMultiTransform 2.1.0" "User Commands"
.SH NAME
WarpTensorImageMultiTransform \- part of ANTS registration suite
.SH DESCRIPTION
WarpImageMultiTransform ImageDimension moving_image output_image [\-R reference_image | \fB\-\-tightest\-bounding\-box]\fR (\fB\-\-reslice\-by\-header\fR) [\-\-use\-NN (use Nearest Neighbor Interpolator)][\-\-ANTS\-prefix prefix\-name | \fB\-\-ANTS\-prefix\-invert\fR prefix\-name] {[deformation_field | [\-i] affine_transform_txt | \fB\-\-Id\fR | [\-i] \fB\-\-moving\-image\-header\fR / \fB\-mh\fR  | [\-i] \fB\-\-reference\-image\-header\fR / \fB\-rh]\fR}
Example:
Reslice the image: WarpImageMultiTransform 3 Imov.nii Iout.nii \fB\-\-tightest\-bounding\-box\fR \fB\-\-reslice\-by\-header\fR
Reslice the image to a reference image: WarpImageMultiTransform 3 Imov.nii Iout.nii \fB\-R\fR Iref.nii \fB\-\-tightest\-bounding\-box\fR \fB\-\-reslice\-by\-header\fR
Note:
\fB\-i\fR will use the inversion of the following affine transform.
\fB\-\-tightest\-bounding\-box\fR will be overrided by \fB\-R\fR reference_image if given. It computes the tightest bounding box using all the affine transformations.
\fB\-\-Id\fR uses the identity transform.
\fB\-\-moving\-image\-header\fR or \fB\-mh\fR in short will use the orientation header of the moving image file. This is typically not used with \fB\-\-reslice\-by\-header\fR.
\fB\-\-reference\-image\-header\fR or \fB\-rh\fR in short will use the orientation header of the fixed image file. This is typically not used with \fB\-\-reslice\-by\-header\fR.
\fB\-\-reslice\-by\-header\fR uses the orientation matrix and origin encoded in the image file header. It can be used together with \fB\-R\fR. This is typically not used together with any other transforms. \fB\-\-reslice\-by\-header\fR is equvalient to \fB\-i\fR \fB\-mh\fR, or \fB\-fh\fR \fB\-i\fR \fB\-mh\fR if used together with \fB\-R\fR.
.PP
For ANTS users:
To use with the deformation field and the affine transform files generated from ANTS:
\fB\-\-ANTS\-prefix\fR prefix\-name
\fB\-\-ANTS\-prefix\-invert\fR prefix\-name
Example:
3 moving_image output_image \fB\-R\fR reference_image \fB\-\-ANTS\-prefix\fR abcd.nii.gz
Applies abcdWarpxvec.nii.gz/abcdWarpyvec.nii.gz/abcdWarpzvec.nii.gz and then abcdAffine.txt. Use this with ANTS to get the moving_image warped into the reference_image domain.
3 reference_image output_image \fB\-R\fR moving_image \fB\-\-ANTS\-prefix\-invert\fR abcd.nii.gz \fB\-\-ANTS\-invert\fR
Applies the inversion of abcdAffine.txt and then abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.nii.gz. Use this with ANTS to get the reference_image warped into the moving_image domain.
Note:
prefix name "abcd" without any extension will use ".nii.gz" by default