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= Name =
mri_register - high-dimensional alignment with canonical atlas

= Synopsis =
mri_register [options] invol refvol outvol

= Arguments =
== Positional Arguments ==
|| invol  || input volume     ||
|| refvol || reference volume ||
|| outvol || output volume    ||

== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
||   -align || ||
||   -T lta || ||
||   -mask <brainmask> || use MR volume brainmask to mask input volume ||
||   -invert-and-save <gcamfile> || load, invert and save gcamfile, then exit||
||   -dist distance || l_dist = distance ||
||   -regularize <reg> || regularize variance to be sigma +reg (noise) ||
||   -regularize-mean <regmean> || regularize means to be regmean u(global) + (1-regmean) u(r)||
||   -scale_smoothness <bool> || scale (or not scale) smooothness coefficient (default=1) setting npasses=2 ||
||   -nobright  || remove bright non-brain structures ||
||   -renormalize || renormalize GCA to MAP estimate of means||
||   -read_lta  || read LTA from <base-name>.lta ||
||   -smoothness <real> || l_smoothness = real ||
||   -samples <cpfile> || write control points to <cpfile> ||
||   -nsmall <int> || allow int small steps before terminating integration||
||   -fixed || use fixed time-step integration ||
||   -optimal || use optimal time-step integration ||
||   -noneg bool || allow or not allow temporary folds during numerical minimization ||
||   -wm || register white matter in initial pass ||
||   -min_avgs <n> || setting min # of averages to n (default 0) ||
||   -tl <file> ||read temporal lobe atlas from <file> ||
||   -relabel bool ||relabel or not relabel nodes with MAP estimates ||
||   -relabel_avgs real || relabel nodes with MAP estimates at avgs=real ||
||   -reset_avgs real || reset metric properties at avgs=real ||
||   -vf <vf_fname> || write vector field to <vf_fname> ||
||   -diag <diagfname> || open diagfname for writing  ||
||   -tr real || use TR=real msec ||
||   -te real || use TE=real msec ||
||   -example <T1> <seg> || use T1 and seg as example T1 and segmentations respectively ||
||   -<no>bigventricles || handle expanded ventricles ||
||   -uncompress || ||
||   -secondpassrenorm || perform 2nd-pass renormalization ||


 
= Outputs =
|| outvol || output volume||

= Description =
??

= Examples =
== Example 1 ==
{{{
mri_ca_register -align -mask brainmask.mgz \
    -T transforms/talairach.lta norm.mgz \
    $FREESURFER_HOME/average/RB_all_2006-02-15.gca \
    transforms/talairach.m3z
}}}

== Example 2 ==
??

= Bugs =
None

= See Also =
[[othercommand1]], [[othercommand2]]

= Links =
FreeSurfer, FsFast

= Methods Description =
{{{
??
}}}

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

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

= Author/s =
BruceFischl