mri_em_register
mri_em_register [options] <in brain volume> <template gca> <output transform name>
This program creates a tranform in lta format
Argument | Explanation |
---|---|
<in brain volume> | input volume |
<template gca> | template gca |
<output transform name> | output transform |
Argument | Explanation |
---|---|
-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 |
Output | Explanation |
---|---|
tranform | transform in lta format |
mri_em_register -mask subject1/mri/brain subject1/mri/nu single_one.gca subject1/mri/transforms/talairach_one.lta
None
Report bugs to <freesurfer@nmr.mgh.harvard.edu>