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| mri_em_register <in brain volume> <template gca> <output transform name> | mri_em_register [options] <in brain volume> <template gca> <output transform name> |
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| || -mask volname ||use volname as a mask || |
|| -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 || |
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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
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>