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.. _ahelp_3dCompareAffine:

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3dCompareAffine
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    Usage: 3dCompareAffine [options]   ~1
    
    This program compares two (or more) affine spatial transformations
    on a dataset, and outputs various measurements of how much these
    transformations differ in spatial displacements.
    
    One use for this program is to compare affine alignment matrices
    from different methods for aligning 3D brain images.
    
    Transformation matrices are specified in a few different ways:
      * ASCII filename containing 12 numbers arranged in 3 lines:
         u11 u12 u13 v1
         u21 u22 u23 v2
         u31 u32 u33 v3
      * ASCII filename containing with 12 numbers in a single line:
         u11 u12 u13 v1 u21 u22 u23 v2 u31 u32 u33 v3
        This is the '.aff12.1D' format output by 3dAllineate,
        and this is the only format that can contain more than
        one matrix in one file.
      * Directly on the command line:
         'MATRIX(u11,u12,u13,v1,u21,u22,u23,v2,u31,u32,u33,v3)'
    
    -------
    Options
    -------
    -mask mmm    = Read in dataset 'mmm' and use non-zero voxels
                   as the region over which to compare the two
                   affine transformations.
                  * You can specify the use of the MNI152 built-in template
                    mask by '-mask MNI152'.
                  * In the future, perhaps other built-in masks will be created?
     *OR*
    -dset ddd    = Read in dataset 'mmm', compute an automask from
                   it (via program 3dAutomask), and use that mask
                   as the spatial region for comparison.
                  * If you don't give EITHER '-mask' or '-dset', then
                    this program will use an internal mask derived from
                    the MNI152 template (skull off).
    
    -affine aaa  = Input an affine transformation (file or 'MATRIX').
     *OR*         * You can give more than one '-affine' option to
    -matrix aaa     input multiple files.
                  * You can also put multiple filenames after the
                    '-affine' option, as in '-affine aaa.aff12.1D bbb.aff12.1D'
                  * The first matrix found in the first '-affine' option
                    is the base transformation to which all following
                    transformations will be compared.
    ------
    Method
    ------
    1) The input mask is hollowed out -- that is, all nonzero mask voxels that
        do NOT neighbor a zero voxel are turned to zero. Thus, only the 'edge'
        voxels are used in the computations below. For example, the default
        MNI152 mask has 1818562 nonzero voxels before hollowing out, and
        has 74668 after hollowing out. The hollowing out algorithm is described
        in the help for program 3dAutomask.
    2) For each surviving voxel, the xyz coordinates are calculated and then
       transformed by the pair of matrices being compared. Then the Euclidean
       distance between these two sets of transformed xyz vectors is calculated.
       The outputs for each comparison are the maximum distance and the
       root-mean-square (RMS) distance, over the set of hollowed out mask voxels.
    
    The purpose of this program is to compare the results from 3dAllineate
    and other registration programs, run under different conditions.
    
    -- Author: RWCox - Mar 2020 at the Tulsa bootcamp