Usage: 3dWarp [options] dataset
Warp (spatially transform) one 3D dataset.

* Here, the 'warp' is a 3x4 matrix = affine transform of space which
  the user supplies.
* Such a transformation can be computed by 3dWarpDrive or 3dAllineate,
  by matching one dataset to another.
* However, 3dAllineate can also transform a dataset given a matrix,
  so the usefulness of these older 3dWarp programs is now limited.
***** For nonlinear spatial warping, see program 3dQwarp. *****
Transform Defining Options: [exactly one of these must be used]
  -matvec_in2out mmm = Read a 3x4 affine transform matrix+vector
                        from file 'mmm':
                         x_out = Matrix x_in + Vector

  -matvec_out2in mmm = Read a 3x4 affine transform matrix+vector
                         from file 'mmm':
                         x_in = Matrix x_out + Vector

     ** N.B.: The coordinate vectors described above are
               defined in DICOM ('RAI') coordinate order.
               (Also see the '-fsl_matvec option, below.)
     ** N.B.: Using the special name 'IDENTITY' for 'mmm'
               means to use the identity matrix.
     ** N.B.: You can put the matrix on the command line
               directly by using an argument of the form
               in place of 'mmm', where the aij values are the
               matrix entries (aij = i-th row, j-th column),
               separated by commas.
             * You will need the 'forward single quotes' around
               the argument.

  -tta2mni = Transform a dataset in Talairach-Tournoux Atlas
              coordinates to MNI-152 coordinates.
  -mni2tta = Transform a dataset in MNI-152 coordinates to
              Talairach-Tournoux Atlas coordinates.

  -matparent mset = Read in the matrix from WARPDRIVE_MATVEC_*
                     attributes in the header of dataset 'mset',
                     which must have been created by program
                     3dWarpDrive.  In this way, you can apply
                     a transformation matrix computed from
                     in 3dWarpDrive to another dataset.

     ** N.B.: The above option is analogous to the -rotparent
                option in program 3drotate.  Use of -matparent
                should be limited to datasets whose spatial
                coordinate system corresponds to that which
                was used for input to 3dWarpDrive (i.e., the
                input to 3dWarp should overlay properly with
                the input to 3dWarpDrive that generated the
                -matparent dataset).

  -card2oblique   obl_dset
  -oblique_parent obl_dset = Read in the oblique transformation matrix
     from an oblique dataset and make cardinal dataset oblique to match.
  -deoblique or
  -oblique2card = Transform an oblique dataset to a cardinal dataset
     Both these oblique transformation options require a new grid for the
     output as specified with the -newgrid or -gridset options
     or a new grid will be assigned based on the minimum voxel spacing
    ** N.B.: EPI time series data should be time shifted with 3dTshift before                rotating the volumes to a cardinal direction

  -disp_obl_xform_only = (new opt) just display the obliquity transform
                         matrix that would be applied to make the output
                         dset;  very useful for moving between oblique
                         coords, such as with '-oblique_parent ..' or
                         '-deoblique'.  The result can be dumped into a
                         text file, e.g.:
                              > textfile.aff12.1D
                         No dataset is created or changed.

Sample usages:
 3dWarpDrive -affine_general -base d1+orig -prefix d2WW -twopass -input d2+orig
 3dWarp -matparent d2WW+orig -prefix epi2WW epi2+orig

 3dWarp -card2oblique oblique_epi+orig -prefix oblique_anat card_anat+orig
 3dWarp -oblique2card -prefix card_epi_tshift -newgrid 3.5 epi_tshift+orig
 3dWarp -card2oblique oblique_epi.nii -disp_obl_transf_only epi_tshift+orig\
        > mat_obl_transform.aff12.1D

Example of warping +tlrc results back to +orig space of some subject
(get xform matrix, apply it, tell dataset it is not in orig space):

    cat_matvec subj1_anat+tlrc::WARP_DATA > tlrc_xform.1D
    3dWarp -matvec_out2in tlrc_xform.1D -prefix group_warped+tlrc \
           -gridset subj1_epi+orig -cubic group_data+tlrc
    3drefit -view orig group_warped+tlrc

Other Transform Options:
  -linear     }
  -cubic      } = Chooses spatial interpolation method.
  -NN         } =   [default = linear]
  -quintic    }
  -wsinc5     }

  -fsl_matvec   = Indicates that the matrix file 'mmm' uses FSL
                    ordered coordinates ('LPI').  For use with
                    matrix files from FSL and SPM.

  -newgrid ddd  = Tells program to compute new dataset on a
                    new 3D grid, with spacing of 'ddd' mmm.
                  * If this option is given, then the new
                    3D region of space covered by the grid
                    is computed by warping the 8 corners of
                    the input dataset, then laying down a
                    regular grid with spacing 'ddd'.
                  * If this option is NOT given, then the
                    new dataset is computed on the old
                    dataset's grid.

  -gridset ggg  = Tells program to compute new dataset on the
                    same grid as dataset 'ggg'.

  -zpad N       = Tells program to pad input dataset with 'N'
                    planes of zeros on all sides before doing
Miscellaneous Options:
  -verb         = Print out some information along the way.
  -prefix ppp   = Sets the prefix of the output dataset.

++ Compile date = Jun 14 2024 {AFNI_24.1.19:linux_ubuntu_16_64}