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= Name =
'''mri_ca_register''' - generates a multi-dimensional talairach transform from a gca file and talairach.lta file

= Synopsis =
mri_ca_register <invol> <template> <outvol>

= Arguments =
== Positional Arguments ==
|| invol || input volume ||
|| template || template in gca format ||
|| outvol || output volume in m3d format ||

== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
|| -tol || defines convergence of registration ||
|| -mask || specifies volume to use as a mask ||
|| -T || transform in lta format ||
|| -level || defines how many surrounding voxels will be used in interpolations, default is 6 ||
|| -ri || allows reading of multiple intensity normalization ||

= Outputs =
|| outvol  || multidimensional transform in m3d format ||

= Examples =
== Example 1 ==
mri_ca_register -levels 6 -mask subject1/mri/brain -T subject1/mri/transforms/talairach_one.lta subject1/mri/norm_one.mgh single_one.gca subject1/mri/transforms/talairach_one.m3d

== Example 2 ==
mri_ca_register -tol 1 -mask subject1/mri/brain -T subject1/mri/transforms/talairach_multi.lta subject1/mri/norm_multi.mgh multi_one.gca subject1/mri/transforms/talairach_multi.m3d

= Links =
FreeSurfer, FsFast

= Methods Description =
[[http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf|Fischl et al. (2004) - See "Nonlinear transform" section]]

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =
BruceFischl