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 >