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mri_robust_register - -mov <mov.mgz> - -dst <dst.mgz> - -lta <m2d.lta> [options] |
{{{ mri_robust_register --mov <mov.mgz> --dst <dst.mgz> --lta <m2d.lta> [options] }}} |
Index
Contents
Name
mri_robust_register - computes symmetric robust registration of two volumes
Synopsis
mri_robust_register --mov <mov.mgz> --dst <dst.mgz> --lta <m2d.lta> [options]
Arguments
Positional Arguments
No positional arguments
Required Flagged Arguments
- -mov <mov.mgz> |
movable input (source) |
source volume as mgz file to be registered |
- -dst <dst.mgz> |
destination input (target) |
target volume as mgz file for the registration |
- -lta <m2d.lta> |
transform output |
gives the xform as lta file (mov to dst) |
Optional Flagged Arguments
- -warp <outvol.mgz> |
warped mov |
apply final xform to source, write to outvol.mgz |
- -weights <wvol.mgz> |
final weights |
output weights transformed to target space as wvol.mgz |
- -halfmov <hm.mgz> |
half-way mov |
outputs half-way mov (mapped to halfway space) |
- -halfdst <hd.mgz> |
half-way dst |
outputs half-way dst (mapped to halfway space) |
- -halfweights <hw.mgz> |
half-way weights |
outputs half-way weights (mapped to halfway space) |
- -halfmovlta <hm.lta> |
half-way mov lta |
outputs transform from mov to half-way space |
- -halfdstlta <hd.lta> |
half-way dst lta |
outputs transform from dst to half-way space |
- -iscale |
intensity scaling |
estimate intensity scale factor (default no I-scaling) |
- -transonly |
only translation |
find 3 parameter translation only |
- -transform <x.lta> |
initial xform |
use initial transform lta on source ('id'=identity), default is geometry (RAS2VOX_dst * VOX2RAS_mov) |
- -initorient |
initial orientation |
use moments for orientation initialization (default false), (recommended for stripped brains, but has difficulties with full head images with different cropping) |
- -vox2vox |
output VOX2VOX |
output VOX2VOX lta file (default is RAS2RAS) |
- -leastsquares |
non-robust |
use least squares instead of robust M-estimator (not recommended, for testing only) |
- -maxit <#> |
max iterations |
iterate max # times on each resolution (default 5) |
- -epsit <float> |
eps change |
stop iterations when change below <float> (default 0.01) |
- -nomulti |
no multiscale |
work on highest resolution |
- -sat <float> |
saturation |
set saturation for robust estimator (default 4.685) |
- -subsample <#> |
subsample image |
subsample if dim > # on all axes (default no subsampling) |
- -maskmov <mask.mgz> |
apply mask mov |
mask mov/src with mask.mgz |
- -maskdst <mask.mgz> |
apply mask dst |
mask dst/target with mask.mgz |
- -uchar |
convert to uchar |
set volumes type to UCHAR (with intens. scaling) |
- -conform |
conform volumes |
conform volumes to 1mm vox (256^3) |
- -satit |
for testing |
iterate on highest res with different sat, for testing only |
- -debug |
print debug info |
show debug output (default no debug output) |
Outputs
See above
Description
This program symmetrically aligns two volumes. It uses a method based on robust statistics to detect outliers and removes them from the registration. This leads to highly accurate registrations even with local changes in the image (e.g. jaw movement). The main purpose is to find the rigid registration (translation, rotation) of longitudinal data, but the method can be used to rigidly align different images. An additional optional intensity scale parameter can be used to adjust for global intensity differences. The extension to affine registration is being tested.
Examples
Example 1
mri_robust_register --mov vol1.mgz --dst vol2.mgz --lta v1to2.lta --warp v1to2.mgz --weights v1to2-weights.mgz --iscale
Computes the rigid registration (6 degrees of freedom) of vol1.mgz to vol2.mgz using robust statistics and with an additional 7th global intensity scaling parameter (recommended e.g. for orig.mgz). The output is the transform (v1to2.lta) and v1to2.mgz (the aligned vol1.mgz to the target image). Additionally the weights of the robust registation (outlier detection) are saved. Everything can be viewed in tkmedit with:
tkmedit -f vol2.mgz -aux v1to2.mgz -overlay v1to2-weights.mgz
Example 2
mri_robust_register --mov vol1.mgz --dst vol2.mgz --lta v1to2.lta --halfmov h1.mgz --halfdst h2.mgz --halfmovlta h1.lta --halfdstlta h2.lta --iscale
Computes the rigid robust registration with intensity scaling of vol1 to vol2 (the registration will be in v1to2.lta). Additionally outputs the half-way volumes h1 and h2 (with corresponding transforms h1.lta and h2.lta). As both volumes are mapped to the half-way space, they will both be resampled. This can be used to construct an unbiased mean volume (e.g. with mri_average) or to compute change maps. The output can be view with:
tkmedit -f h1.mgz -aux h2.mgz
Bugs
None (of course)
See Also
Links
Methods Description
description description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>