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'''Index'''
<<TableOfContents>>


= 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 =
FreeSurfer, FsFast

= Methods Description =
[[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf|Fischl et al., 2002 - See "Optimal Linear Transform" section]]

= References =
[[References/Lastname###]]

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =