AFNI program: 3drefit

Changes some of the information inside a 3D dataset's header.
Note that this program does NOT change the .BRIK file at all;
the main purpose of 3drefit is to fix up errors made when
using to3d.
To see the current values stored in a .HEAD file, use the command
'3dinfo dataset'.  Using 3dinfo both before and after 3drefit is
a good idea to make sure the changes have been made correctly!

Usage: 3drefit [options] dataset ...
where the options are
  -orient code    Sets the orientation of the 3D volume(s) in the .BRIK.
                  The code must be 3 letters, one each from the
                  pairs {R,L} {A,P} {I,S}.  The first letter gives
                  the orientation of the x-axis, the second the
                  orientation of the y-axis, the third the z-axis:
                     R = right-to-left         L = left-to-right
                     A = anterior-to-posterior P = posterior-to-anterior
                     I = inferior-to-superior  S = superior-to-inferior
               ** WARNING: when changing the orientation, you must be sure
                  to check the origins as well, to make sure that the volume
                  is positioned correctly in space.

  -xorigin distx  Puts the center of the edge voxel off at the given
  -yorigin disty  distance, for the given axis (x,y,z); distances in mm.
  -zorigin distz  (x=first axis, y=second axis, z=third axis).
                  Usually, only -zorigin makes sense.  Note that this
                  distance is in the direction given by the corresponding
                  letter in the -orient code.  For example, '-orient RAI'
                  would mean that '-zorigin 30' sets the center of the
                  first slice at 30 mm Inferior.  See the to3d manual
                  for more explanations of axes origins.
               ** SPECIAL CASE: you can use the string 'cen' in place of
                  a distance to force that axis to be re-centered.

 -xorigin_raw xx  Puts the center of the edge voxel at the given COORDINATE
 -yorigin_raw yy  rather than the given DISTANCE.  That is, these values
 -zorigin_raw zz  directly replace the offsets in the dataset header,
                  without any possible sign changes.

  -duporigin cset Copies the xorigin, yorigin, and zorigin values from
                  the header of dataset 'cset'.

  -dxorigin dx    Adds distance 'dx' (or 'dy', or 'dz') to the center
  -dyorigin dy    coordinate of the edge voxel.  Can be used with the
  -dzorigin dz    values input to the 'Nudge xyz' plugin.
               ** WARNING: you can't use these options at the same
                  time you use -orient.

  -xdel dimx      Makes the size of the voxel the given dimension,
  -ydel dimy      for the given axis (x,y,z); dimensions in mm.
  -zdel dimz   ** WARNING: if you change a voxel dimension, you will
                  probably have to change the origin as well.

  -TR time        Changes the TR time to a new value (see 'to3d -help').
  -notoff         Removes the slice-dependent time-offsets.
  -Torg ttt       Set the time origin of the dataset to value 'ttt'.
                  (Time origins are set to 0 in to3d.)
               ** WARNING: these 3 options apply only to 3D+time datasets.

  -newid          Changes the ID code of this dataset as well.

  -nowarp         Removes all warping information from dataset.

  -apar aset      Set the dataset's anatomy parent dataset to 'aset'
               ** N.B.: The anatomy parent is the dataset from which the
                  transformation from +orig to +acpc and +tlrc coordinates
                  is taken.  It is appropriate to use -apar when there is
                  more than 1 anatomical dataset in a directory that has
                  been transformed.  In this way, you can be sure that
                  AFNI will choose the correct transformation.  You would
                  use this option on all the +orig dataset that are
                  aligned with 'aset' (i.e., that were acquired in the
                  same scanning session).
               ** N.B.: Special cases of 'aset'
                   aset = NULL --> remove the anat parent info from the dataset
                   aset = SELF --> set the anat parent to be the dataset itself

  -clear_bstat    Clears the statistics (min and max) stored for each sub-brick
                  in the dataset.  This is useful if you have done something to
                  modify the contents of the .BRIK file associated with this
                  dataset.

  -statpar v ...  Changes the statistical parameters stored in this
                  dataset.  See 'to3d -help' for more details.

  -markers        Adds an empty set of AC-PC markers to the dataset,
                  if it can handle them (is anatomical, is in the +orig
                  view, and isn't 3D+time).
               ** WARNING: this will erase any markers that already exist!

  -view code      Changes the 'view' to be 'code', where the string 'code'
                  is one of 'orig', 'acpc', or 'tlrc'.
               ** WARNING: The program will also change the .HEAD and .BRIK
                  filenames to match.  If the dataset filenames already
                  exist in the '+code' view, then this option will fail.
                  You will have to rename the dataset files before trying
                  to use '-view'.  If you COPY the files and then use
                  '-view', don't forget to use '-newid' as well!

  -byteorder bbb  Sets the byte order string in the header.
                  Allowable values for 'bbb' are:
                     LSB_FIRST   MSB_FIRST   NATIVE_ORDER
                  Note that this does not change the .BRIK file!
                  This is done by programs 2swap and 4swap.

  -appkey ll      Appends the string 'll' to the keyword list for the
                  whole dataset.
  -repkey ll      Replaces the keyword list for the dataset with the
                  string 'll'.
  -empkey         Destroys the keyword list for the dataset.

  -'type'         Changes the type of data that is declared for this
                  dataset, where 'type' is chosen from the following:
       ANATOMICAL TYPES
         spgr == Spoiled GRASS             fse == Fast Spin Echo  
         epan == Echo Planar              anat == MRI Anatomy     
           ct == CT Scan                  spct == SPECT Anatomy   
          pet == PET Anatomy               mra == MR Angiography  
         bmap == B-field Map              diff == Diffusion Map   
         omri == Other MRI                abuc == Anat Bucket     
       FUNCTIONAL TYPES
          fim == Intensity                fith == Inten+Thr       
         fico == Inten+Cor                fitt == Inten+Ttest     
         fift == Inten+Ftest              fizt == Inten+Ztest     
         fict == Inten+ChiSq              fibt == Inten+Beta      
         fibn == Inten+Binom              figt == Inten+Gamma     
         fipt == Inten+Poisson            fbuc == Func-Bucket     
-copyaux auxset   Copies the 'auxiliary' data from dataset 'auxset'
                  over the auxiliary data for the dataset being
                  modified.  Auxiliary data comprises sub-brick labels,
                  keywords, and statistics codes.
                  '-copyaux' occurs BEFORE the '-sub' operations below,
                  so you can use those to alter the auxiliary data
                  that is copied from auxset.

The options below allow you to attach auxiliary data to sub-bricks
in the dataset.  Each option may be used more than once so that
multiple sub-bricks can be modified in a single run of 3drefit.

  -sublabel  n ll  Attach to sub-brick #n the label string 'll'.
  -subappkey n ll  Add to sub-brick #n the keyword string 'll'.
  -subrepkey n ll  Replace sub-brick #n's keyword string with 'll'.
  -subempkey n     Empty out sub-brick #n' keyword string

  -substatpar n type v ...
                  Attach to sub-brick #n the statistical type and
                  the auxiliary parameters given by values 'v ...',
                  where 'type' is one of the following:
         type  Description  PARAMETERS
         ----  -----------  ----------------------------------------
         fico  Cor          SAMPLES  FIT-PARAMETERS  ORT-PARAMETERS
         fitt  Ttest        DEGREES-of-FREEDOM
         fift  Ftest        NUMERATOR and DENOMINATOR DEGREES-of-FREEDOM
         fizt  Ztest        N/A
         fict  ChiSq        DEGREES-of-FREEDOM
         fibt  Beta         A (numerator) and B (denominator)
         fibn  Binom        NUMBER-of-TRIALS and PROBABILITY-per-TRIAL
         figt  Gamma        SHAPE and SCALE
         fipt  Poisson      MEAN

The following options allow you to modify VOLREG fields:
  -vr_mat  ...    Use these twelve values for VOLREG_MATVEC_index.
  [-vr_mat_ind ]        Index of VOLREG_MATVEC_index field to be modified. Optional, default index is 0.
                               Note: You can only modify one VOLREG_MATVEC_index at a time.
  -vr_center_old      Use these 3 values for VOLREG_CENTER_OLD.
  -vr_center_base     Use these 3 values for VOLREG_CENTER_BASE.

		Last modified: Oct 04/02.