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>