Index
Contents
Name
mri_em_register - creates a tranform in lta format
Synopsis
mri_em_register [options] <in brain volume> <template gca> <output transform name>
Arguments
Positional Arguments
<in brain volume> |
input volume |
<template gca> |
template gca |
<output transform name> |
output transform |
Optional Flagged Arguments
-dist distance |
|
-nomap |
|
-flash |
use FLASH forward model to predict intensity values |
-mask <volname> |
use volname as a mask |
-skull |
align to atlas containing skull (uns=5) |
-uns nbrspacing |
align to atlas containing skull setting unknown_nbr_spacing = nbrspacing |
-diag diagfile |
open diagfile for writing |
-debug_voxel x y z |
debug voxel (x, y, z) |
-debug_label label |
debug label (label) |
-tr TR |
use TR msec |
-te TE |
use TE msec |
-alpha alpha |
use alpha degrees |
-example T1 seg |
use T1 and seg as example T1 and segmentations respectively |
-samples fname |
write control points to fname |
-fsamples fname |
write transformed control points to fname |
-nsamples fname |
write transformed normalization control points to fname |
-contrast |
use contrast to find labels |
-flash_parms parameterfile |
use FLASH forward model and tissue parms in parameterfile to predict intensity values |
-transonly |
only compute translation parameters |
-write_mean fname |
write gca means to fname |
-prior min_prior |
use prior threshold min_prior |
-spacing <int> |
use max GCA spacing |
-scales <int> |
find optimal linear transform over int scales |
-novar |
do not use variance estimates |
-dt dt |
|
-tol tol |
|
-center |
use GCA centroid as origin of transform |
-noscale |
disable scaling |
-noiscale |
disable intensity scaling |
-num num_xforms |
find a total of num_xforms linear transforms |
-area area |
|
-nlarea nlarea |
|
-levels levels |
|
-intensity intensity |
|
-reduce nreductions |
reduce input images nreductions times before aligning |
-nsamples nsamples |
using n samples of GCA |
-norm fname |
normalize intensity and write to fname |
-trans max_trans |
setting max translation search range to be max_trans |
-steps max_angles |
taking max_angles angular steps |
-l xform long_reg |
Longitudinal: read previously computed atlas xform and apply registration long_reg |
-f cpfile |
read manually defined control points from cpfile |
-d tx ty tz |
|
-r rx ry rz |
|
-t xform |
using previously computed transform xform |
-b blur_sigma |
blurring input image with sigma=blur_sigma |
-v diagno |
|
-s max_angles |
|
-max_angle max_angle |
max_angle for rotational search in radians (def=15 deg) |
-n niters |
niterations = niters |
-w write_iters |
write iterations = write_iters |
-p ctl_point_pct |
use top pct percent wm points as control points |
-m momentum |
set momentum |
Outputs
tranform |
transform in lta format |
Description
Examples
Example 1
mri_em_register -mask subject1/mri/brain subject1/mri/nu single_one.gca subject1/mri/transforms/talairach_one.lta
Bugs
none known
See Also
Links
Methods Description
Fischl et al., 2002 - See "Optimal Linear Transform" section
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>