Usage: 3dvolreg [options] dataset

* Registers each 3D sub-brick from the input dataset to the base brick.
  'dataset' may contain a sub-brick selector list.

* This program is written to be fast, and is limited to rigid body
  (6 parameter) transformations.

-->> Also see the script align_epi_anat.py for a more general
     alignment procedure, which does not require that the base
     and source datasets be defined on the same 3D grid.
-->> Program 3dQwarp can do nonlinear warping of one dataset
     to match another.
-->> datasets.  Script @2dwarper.Allin can do nonlinear
     warping in 2D to align 2 datasets on a slice-wise basis
     (no out-of-slice movements; each slice registered separately).

  -verbose        Print progress reports.  Use twice for LOTS of output.
  -Fourier        Perform the alignments using Fourier interpolation.
  -heptic         Use heptic polynomial interpolation.
  -quintic        Use quintic polynomical interpolation.
  -cubic          Use cubic polynomial interpolation.
  -linear         Use linear interpolation.
             -->>   OLD Default = Fourier [slowest and most accurate interpolator]
             -->>   NEW Default = Heptic [7th order polynomials]
  -clipit         Clips the values in each output sub-brick to be in the same
                    range as the corresponding input volume.
                    The interpolation schemes can produce values outside
                    the input range, which is sometimes annoying.
                    [16 Apr 2002: -clipit is now the default]
  -noclip         Turns off -clipit
  -zpad n         Zeropad around the edges by 'n' voxels during rotations
                    (these edge values will be stripped off in the output)
              N.B.: Unlike to3d, in this program '-zpad' adds zeros in
                     all directions.
              N.B.: The environment variable AFNI_ROTA_ZPAD can be used
                     to set a nonzero default value for this parameter.
              N.B.: [22 May 2019] The default value for zero padding
                    is now set to 4 voxels on each of the 6 planes.
  -prefix fname   Use 'fname' for the output dataset prefix.
                    The program tries not to overwrite an existing dataset.
                    Default = 'volreg'.
              N.B.: If the prefix is 'NULL', no output dataset will be written.

  -float          Force output dataset to be written in floating point format.
              N.B.: If the input dataset has scale factors attached to ANY
                    sub-bricks, then the output will always be written in
                    float format!

  -base n         Sets the base brick to be the 'n'th sub-brick
                    from the input dataset (indexing starts at 0).
                    Default = 0 (first sub-brick).
  -base 'bset[n]' Sets the base brick to be the 'n'th sub-brick
                    from the dataset specified by 'bset', as in
                       -base 'elvis+orig[4]'
                    The quotes are needed because the '[]' characters
                    are special to the command line shell.

  -dfile dname    Save the motion parameters in file 'dname'.
                    The output is in 9 ASCII formatted columns:

                    n  roll  pitch  yaw  dS  dL  dP  rmsold rmsnew

           where:   n     = sub-brick index
                    roll  = rotation about the I-S axis }
                    pitch = rotation about the R-L axis } degrees CCW
                    yaw   = rotation about the A-P axis }
                      dS  = displacement in the Superior direction  }
                      dL  = displacement in the Left direction      } mm
                      dP  = displacement in the Posterior direction }
                   rmsold = RMS difference between input brick and base brick
                   rmsnew = RMS difference between output brick and base brick
       N.B.: If the '-dfile' option is not given, the parameters aren't saved.
       N.B.: The motion parameters are those needed to bring the sub-brick
             back into alignment with the base.  In 3drotate, it is as if
             the following options were applied to each input sub-brick:
              -rotate 'roll'I 'pitch'R 'yaw'A  -ashift 'dS'S 'dL'L 'dP'P
       ** roll  = shaking head 'no' left-right
       ** pitch = nodding head 'yes' up-down
       ** yaw   = wobbling head sideways (ear toward shoulder)

  -1Dfile ename   Save the motion parameters ONLY in file 'ename'.
                    The output is in 6 ASCII formatted columns:

                    roll pitch yaw dS  dL  dP

                  This file can be used in FIM as an 'ort', to detrend
                  the data against correlation with the movements.
                  This type of analysis can be useful in removing
                  errors made in the interpolation.

  -1Dmatrix_save ff = Save the matrix transformation from base to input
                      coordinates in file 'ff' (1 row per sub-brick in
                      the input dataset).  If 'ff' does NOT end in '.1D',
                      then the program will append '.aff12.1D' to 'ff' to
                      make the output filename.
               *N.B.: This matrix is the coordinate transformation from base
                      to input DICOM coordinates.  To get the inverse matrix
                      (input to base), use the cat_matvec program, as in
                        cat_matvec fred.aff12.1D -I
               *N.B.: This matrix is the inverse of the matrix stored in
                      the output dataset VOLREG_MATVEC_* attributes.
                      The base-to-input convention followed with this
                      option corresponds to the convention in 3dAllineate.
               *N.B.: 3dvolreg does not have a '-1Dmatrix_apply' option.
                      See 3dAllineate for this function.  Also confer with
                      program cat_matvec.

  -rotcom         Write the fragmentary 3drotate commands needed to
                  perform the realignments to stdout; for example:
                    3drotate -rotate 7.2I 3.2R -5.7A -ashift 2.7S -3.8L 4.9P
                  The purpose of this is to make it easier to shift other
                  datasets using exactly the same parameters.

  -maxdisp      = Print the maximum displacement (in mm) for brain voxels.
                    ('Brain' here is defined by the same algorithm as used
                    in the command '3dAutomask -clfrac 0.33'; the displacement
                    for each non-interior point in this mask is calculated.)
                    If '-verbose' is given, the max displacement will be
                    printed to the screen for each sub-brick; otherwise,
                    just the overall maximum displacement will get output.
                 ** This displacement is relative to the base volume.
                    [-maxdisp is now turned on by default]
  -nomaxdisp    = Do NOT calculate and print the maximum displacement.
                    [maybe it offends you in some theological sense?]
                    [maybe you have some real 'need for speed'?]
  -maxdisp1D mm = Do '-maxdisp' and also write the max displacement for each
                    sub-brick into file 'mm' in 1D (columnar) format.
                    You may find that graphing this file (cf. 1dplot)
                    is a useful diagnostic tool for your FMRI datasets.
                    [the 'mm' filename can be '-', which means stdout]
                 ** The program also outputs the maximum change (delta) in
                    displacement between 2 successive time points, into the
                    file with name 'mm_delt'.  This output can let you see
                    when there is a sudden head jerk, for example. [22 Jun 2015]

  -savedisp sss = Save 3 3D+time datasets with the x,y,z displacments at each
                  voxel at each time point.  The prefix for the x displacement
                  dataset will be the string 'sss' with '_DX' appended, etc.
                  This option is intended for use with various processing
                  scripts now under construction, and is probably otherwise
                  completely useless.

  -tshift ii      If the input dataset is 3D+time and has slice-dependent
                  time-offsets (cf. the output of 3dinfo -v), then this
                  option tells 3dvolreg to time shift it to the average
                  slice time-offset prior to doing the spatial registration.
                  The integer 'ii' is the number of time points at the
                  beginning to ignore in the time shifting.  The results
                  should like running program 3dTshift first, then running
                  3dvolreg -- this is primarily a convenience option.
            N.B.: If the base brick is taken from this dataset, as in
                  '-base 4', then it will be the time shifted brick.
                  If for some bizarre reason this is undesirable, you
                  could use '-base this+orig[4]' instead.

  -rotparent rset
    Specifies that AFTER the registration algorithm finds the best
    transformation for each sub-brick of the input, an additional
    rotation+translation should be performed before computing the
    final output dataset; this extra transformation is taken from
    the first 3dvolreg transformation found in dataset 'rset'.
  -gridparent gset
    Specifies that the output dataset of 3dvolreg should be shifted to
    match the grid of dataset 'gset'.  Can only be used with -rotparent.
    This dataset should be one this is properly aligned with 'rset' when
    overlaid in AFNI.
  * If 'gset' has a different number of slices than the input dataset,
    then the output dataset will be zero-padded in the slice direction
    to match 'gset'.
  * These options are intended to be used to align datasets between sessions:
     S1 = SPGR from session 1    E1 = EPI from session 1
     S2 = SPGR from session 2    E2 = EPI from session 2
 3dvolreg -twopass -twodup -base S1+orig -prefix S2reg S2+orig
 3dvolreg -rotparent S2reg+orig -gridparent E1+orig -prefix E2reg \
          -base 4 E2+orig
     Each sub-brick in E2 is registered to sub-brick E2+orig[4], then the
     rotation from S2 to S2reg is also applied, which shifting+padding
     applied to properly overlap with E1.
  * A similar effect could be done by using commands
 3dvolreg -twopass -twodup -base S1+orig -prefix S2reg S2+orig
 3dvolreg -prefix E2tmp -base 4 E2+orig
 3drotate -rotparent S2reg+orig -gridparent E1+orig -prefix E2reg E2tmp+orig
    The principal difference is that the latter method results in E2
    being interpolated twice to make E2reg: once in the 3dvolreg run to
    produce E2tmp, then again when E2tmp is rotated to make E2reg.  Using
    3dvolreg with the -rotparent and -gridparent options simply skips the
    intermediate interpolation.

          *** Please read file README.registration for more   ***
          *** information on the use of 3dvolreg and 3drotate ***

 Algorithm: Iterated linearized weighted least squares to make each
              sub-brick as like as possible to the base brick.
              This method is useful for finding SMALL MOTIONS ONLY.
              See program 3drotate for the volume shift/rotate algorithm.
              The following options can be used to control the iterations:
                -maxite     m = Allow up to 'm' iterations for convergence
                                  [default = 23].
                -x_thresh   x = Iterations converge when maximum movement
                                  is less than 'x' voxels [default=0.010000],
                -rot_thresh r = And when maximum rotation is less than
                                  'r' degrees [default=0.020000].
                -delta      d = Distance, in voxel size, used to compute
                                  image derivatives using finite differences
                -final   mode = Do the final interpolation using the method
                                  defined by 'mode', which is one of the
                                  strings 'NN', 'cubic', 'quintic', 'heptic',
                                  or 'Fourier' or 'linear'
                                  [default=mode used to estimate parameters].
            -weight 'wset[n]' = Set the weighting applied to each voxel
                                  proportional to the brick specified here
                                  [default=smoothed base brick].
                                N.B.: if no weight is given, and -twopass is
                                  engaged, then the first pass weight is the
                                  blurred sum of the base brick and the first
                                  data brick to be registered.
                   -edging ee = Set the size of the region around the edges of
                                  the base volume where the default weight will
                                  be set to zero.  If 'ee' is a plain number,
                                  then it is a voxel count, giving the thickness
                                  along each face of the 3D brick.  If 'ee' is
                                  of the form '5%', then it is a fraction of
                                  of each brick size.  For example, '5%' of
                                  a 256x256x124 volume means that 13 voxels
                                  on each side of the xy-axes will get zero
                                  weight, and 6 along the z-axis.  If this
                                  option is not used, then 'ee' is read from
                                  the environment variable AFNI_VOLREG_EDGING.
                                  If that variable is not set, then 5% is used.
                                N.B.: This option has NO effect if the -weight
                                  option is used.
                                N.B.: The largest % value allowed is 25%.
                     -twopass = Do two passes of the registration algorithm:
                                 (1) with smoothed base and data bricks, with
                                     linear interpolation, to get a crude
                                     alignment, then
                                 (2) with the input base and data bricks, to
                                     get a fine alignment.
                                  This method is useful when aligning high-
                                  resolution datasets that may need to be
                                  moved more than a few voxels to be aligned.
                  -twoblur bb = 'bb' is the blurring factor for pass 1 of
                                  the -twopass registration.  This should be
                                  a number >= 2.0 (which is the default).
                                  Larger values would be reasonable if pass 1
                                  has to move the input dataset a long ways.
                                  Use '-verbose -verbose' to check on the
                                  iterative progress of the passes.
                                N.B.: when using -twopass, and you expect the
                                  data bricks to move a long ways, you might
                                  want to use '-heptic' rather than
                                  the default '-Fourier', since you can get
                                  wraparound from Fourier interpolation.
                      -twodup = If this option is set, along with -twopass,
                                  then the output dataset will have its
                                  xyz-axes origins reset to those of the
                                  base dataset.  This is equivalent to using
                                  '3drefit -duporigin' on the output dataset.
                       -sinit = When using -twopass registration on volumes
                                  whose magnitude differs significantly, the
                                  least squares fitting procedure is started
                                  by doing a zero-th pass estimate of the
                                  scale difference between the bricks.
                                  Use this option to turn this feature OFF.
              -coarse del num = When doing the first pass, the first step is
                                  to do a number of coarse shifts in order to
                                  find a starting point for the iterations.
                                  'del' is the size of these steps, in voxels;
                                  'num' is the number of these steps along
                                  each direction (+x,-x,+y,-y,+z,-z).  The
                                  default values are del=10 and num=2.  If
                                  you don't want this step performed, set
                                  num=0.  Note that the amount of computation
                                  grows as num**3, so don't increase num
                                  past 4, or the program will run forever!
                             N.B.: The 'del' parameter cannot be larger than
                                   10% of the smallest dimension of the input
              -coarserot        Also do a coarse search in angle for the
                                  starting point of the first pass.
              -nocoarserot      Don't search angles coarsely.
                                  [-coarserot is now the default - RWCox]
              -wtinp          = Use sub-brick[0] of the input dataset as the
                                  weight brick in the final registration pass.

 N.B.: * This program can consume VERY large quantities of memory.
          (Rule of thumb: 40 bytes per input voxel.)
          Use of '-verbose -verbose' will show the amount of workspace,
          and the steps used in each iteration.
       * ALWAYS check the results visually to make sure that the program
          wasn't trapped in a 'false optimum'.
       * The default rotation threshold is reasonable for 64x64 images.
          You may want to decrease it proportionally for larger datasets.
       * -twopass resets the -maxite parameter to 66; if you want to use
          a different value, use -maxite AFTER the -twopass option.
       * The -twopass option can be slow; several CPU minutes for a
          256x256x124 volume is a typical run time.
       * After registering high-resolution anatomicals, you may need to
          set their origins in 3D space to match.  This can be done using
          the '-duporigin' option to program 3drefit, or by using the
          '-twodup' option to this program.

++ Compile date = Jan 27 2020 {AFNI_20.0.03:linux_ubuntu_16_64}