'''Index''' <<TableOfContents>>

= Name =
mri_concatenate_gcam

= Description =
Concatenates a combination of input LTAs (linear transform array) and GCAMs (Gaussian classifier atlas, M3Z).

The passed transforms are applied in the order specified on the command line, i.e. the first transform would be applied to images first - but to coordinates last, as transforms applied to coordinates are the inverse of those applied to images.

Note that binaries such as mri_convert or mri_vol2vol ignore source and target geometries of M3Zs. To morph an image from or to a different space, the M3Z geometry needs to be changed first.

= Synopsis =
mri_concatenate_gcam [options] <input 1> ... <output>

= Arguments =
== Positional Arguments ==
|| input  || Combination of LTAs and M3Zs ||
|| output || Concatenated output transform, saved as an LTA or M3Z depending on the input transforms ||

== Optional Flagged Arguments ==
||'''Flag''' ||'''Description''' ||
||-s, --change-source <source image> || Change source image geometry of output M3Z, useful e.g. for GCAM inversion if the path of the original source volume changed; the warp is modified accordingly ||
||-t, --change-target <target image> || Change destination image geometry of output M3Z; the warp is modified accordingly ||
||-r, --reduce || Reduce output LTA to single LT ||
||-i, --invert || Invert the output transform ||
||-d, --downsample || Downsample output M3Z to spacing of 2; by default, the output spacing is that of the rightmost input M3Z ||

== Outputs ==
||output || Composite LTA or M3Z transform, depending on input ||

= Examples =
== Example 1 ==
Reduce and invert LTA:
{{{
mri_concatenate_gcam -r -i in.lta out.lta
}}}

== Example 2 ==
Concatenate transforms:
{{{
mri_concatenate_gcam in1.fslmat in2.m3z in3.m3z in4.lta out.m3z
}}}

== Example 3 ==
Change M3Z to reflect different source image geometry:
{{{
mri_concatenate_gcam -s norm.nii in.m3z out.m3z
}}}


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

= See Also =
[[lta_convert]] (convert between different linear transform formats)

[[mri_concatenate_lta]] (concatenate or invert LTA transforms)

[[mri_warp_convert]] (similar functionality for warp fields)

[[mri_convert]] -at or -ait (apply transforms to an image)