Align EPI to anatomical datasets or vice versa


. align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 0 -anat2epi

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    REQUIRED OPTIONS:
    -epi dset   : name of EPI dataset
    -anat dset  : name of structural dataset
    -epi_base   : the epi base used in alignment 
                     (0/mean/median/max/subbrick#)
    MAJOR OPTIONS:
    -anat2epi   : align anatomical to EPI dataset (default)
    -epi2anat   : align EPI to anatomical dataset

   Alternative cost functions and methods:
    -cost xxx : 
     ls   *OR*  leastsq         = Least Squares [Pearson Correlation]
     mi   *OR*  mutualinfo      = Mutual Information [H(b)+H(s)-H(b,s)]
     crM  *OR*  corratio_mul    = Correlation Ratio (Symmetrized*)
     nmi  *OR*  norm_mutualinfo = Normalized MI [H(b,s)/(H(b)+H(s))]
     hel  *OR*  hellinger       = Hellinger metric
     crA  *OR*  corratio_add    = Correlation Ratio (Symmetrized+)
     crU  *OR*  corratio_uns    = Correlation Ratio (Unsym)
     lpc  *OR*  localPcorSigned = Local Pearson Correlation Signed
     lpa  *OR*  localPcorAbs    = Local Pearson Correlation Abs
     lpc+ *OR*  localPcor+Others= Local Pearson Signed + Others
     lpa+ *OR*  localPcorAbs+Others= Local Pearson Abs + Others

    -big_move   : indicates that large displacement is needed to align the
                  two volumes. This option is off by default.
    -giant_move : even larger movement required - uses cmass, two passes and
                  very large angles and shifts. May miss finding the solution
                  in the vastness of space, so use with caution
    -ginormous_move : adds align_centers to giant_move. Useful for very far
                  apart datasets