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= See Also = [[mri_concatenate_lta]] (concatenate or invert LTA transforms) [[mri_convert]] -at or -ait (apply transforms to an image) [[mri_warp_convert]] (similar functionality for warp fields) |
Index
Contents
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
mri_concatenate_lta (concatenate or invert LTA transforms)
mri_convert -at or -ait (apply transforms to an image)
mri_warp_convert (similar functionality for warp fields)