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

Software version described:
 * $Date: 2007/12/28 00:49:46 $
 * $Revision: 1.50 $
 * Use usage or version option to see version you are using

= Name =
mris_register - This program registers a surface to an average surface template. Related concepts are discussed here: SurfaceRegAndTemplates.

= Synopsis =
 mris_register [options] <input surface> <input target template or surface> <output surface>

= Arguments =
== Positional Arguments ==
||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''||
||<^>1||<^> <surf_fname> ||<^>Input: Surface to register, often {hemi}.sphere||
||<^>2||<^> <target> ||<^>Input: The data to register to. In normal recon-all usage, this is a template file for average surface. Alternatively could also be a single-subject's surface -- see argument '-1' (one), which is useful during the template-development process. ||
||<^>3||<^> <out_fname> ||<^>Output surface file to capture registration. Example: {hemi}.sphere.reg||

== Required Flagged Arguments ==
|| -flag1 ?? || brief description ||   ||
|| -flag2 ?? || brief description ||   ||

== Optional Flagged Arguments ==
||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''||
||<^>Input||<^>-1||<^> ||<^>(One) Treats target argument as the name of as a single subject's surface not a template file. (What pattern of filename is required?)||
||<^>Input||<^>-addframe||<^> <which_field, where_in_atlas (ints)> ||<^>Add field which_field with location where_in_atlas in the atlas||
||<^>Input||<^>-annot||<^> <annot_name> ||<^>Zeroes medial wall  using annotation {annot_name}||
||<^>Input||<^>-C||<^> <curvature_fname> ||<^>||
||<^>Input||<^>-canon||<^> <canon_name> ||<^>Use surface {canon_name} for canonical properties||
||<^>Input||<^>-inflated||<^> ||<^>Use inflated surface for initial alignment||
||<^>Input||<^>-infname||<^> <name> ||<^>Uses {name} for inflated surface, for initial alignment. Sets inflated_name, surface_name and curvature_names[0]||
||<^>Input||<^>-L||<^> <labelfile atlas_gcsa_file label_name> ||<^>Specify a manual label to align with atlas label <label name>||
||<^>Input||<^>-O||<^> <orig_name> ||<^>Use {orig_name} for original properties||
||<^>Input||<^>-overlay||<^> <overlay_file navgs(int)> ||<^>Adds a variable to the atlas from {overlay_file}, smoothing it {navgs} times. {subject}/labels/{hemi}.{overlay_file}||
||<^>Input||<^>-overlay-dir||<^> <overlay_dir> ||<^>Changes overlay path: {subject}/{overlay_dir}/{hemi}.{overlay_file}||
||<^>Input||<^>-sreg||<^> <starting_reg_fname> ||<^>Start registration with coordinates in file starting_reg_fname||
||<^>Output||<^>-jacobian||<^> <jacobian_fname> ||<^>Write out jacobian of mapping to file jacobian_fname||
||<^>Algorithm||<^>-A||<^> <n_averages (int)> ||<^>||
||<^>Algorithm||<^>-adaptive||<^> ||<^>Use adaptive time step integration||
||<^>Algorithm||<^>-area||<^> <l_area (float)> ||<^>Sets l_area||
||<^>Algorithm||<^>-corr||<^> <l_corr (float)> ||<^>||
||<^>Algorithm||<^>-curv||<^> ||<^>Use smoothwm curvature for final alignment||
||<^>Algorithm||<^>-dist||<^> <l_dist (float)> ||<^>Specify distance term. Sets l_dist and also use_defaults = 0||
||<^>Algorithm||<^>-dt||<^> <dt (float)> ||<^>Sets momentum with dt||
||<^>Algorithm||<^>-dt_dec||<^> <dt_decrease (float)> ||<^>||
||<^>Algorithm||<^>-dt_inc||<^> <dt_increase (float)> ||<^>||
||<^>Algorithm||<^>-E||<^> <l_external (float)> ||<^>||
||<^>Algorithm||<^>-error_ratio||<^> <error_ratio (float)> ||<^>||
||<^>Algorithm||<^>-init||<^> ||<^>Use initial registration||
||<^>Algorithm||<^>-lap||<^> <lap (float)> ||<^>l_laplacian||
||<^>Algorithm||<^>-lm||<^> ||<^>Integrate using line minimization||
||<^>Algorithm||<^>-M||<^> <momentum (float)> ||<^>Chooses integration_type = INTEGRATE_MOMENTUM and sets momentum value||
||<^>Algorithm||<^>-max_degrees||<^> <max_degrees (float)> ||<^>Set max angle for search to max_degrees||
||<^>Algorithm||<^>-median||<^> ||<^>Uses median normalization (instead of mean).||
||<^>Algorithm||<^>-min_degrees||<^> <min_degrees (float)> ||<^>Set min angle for search to min_degrees||
||<^>Algorithm||<^>-multi_scale||<^> <multi_scale (int)> ||<^>Use multi_scale scales for morphing||
||<^>Algorithm||<^>-N||<^> <niterations (int)> ||<^>||
||<^>Algorithm||<^>-nangles||<^> <nangles (int)> ||<^>Set # of angles/search per scale to nangles||
||<^>Algorithm||<^>-nbrs||<^> <nbrs (int)> ||<^>Use neighborhood size=nbrs||
||<^>Algorithm||<^>-nlarea||<^> <l_nlarea (float)> ||<^>Sets l_nlarea||
||<^>Algorithm||<^>-nocurv||<^> ||<^>Do not use smoothwm curvature for final alignment||
||<^>Algorithm||<^>-nonorm||<^> ||<^>Disables normalization||
||<^>Algorithm||<^>-norot||<^> ||<^>Disables initial rigid alignment||
||<^>Algorithm||<^>-nosulc||<^> ||<^>Disables initial sulc alignment||
||<^>Algorithm||<^>-nsurfaces||<^> <nsurfaces> ||<^>Use nsurfaces surfaces/curvatures for alignment||
||<^>Algorithm||<^>-ocorr||<^> <l_ocorr (float)> ||<^>Sets overlay correlation coefficient to l_ocorr||
||<^>Algorithm||<^>-P||<^> <max_passes (int)> ||<^>Limit unfolding to {max_passes} passes||
||<^>Algorithm||<^>-parea||<^> <l_parea (float)> ||<^>Sets l_parea||
||<^>Algorithm||<^>-remove_negative||<^> <remove_negative (int)> ||<^>Non-zero to remove negative triangles with iterative smoothing, or 0 to skip that||
||<^>Algorithm||<^>-reverse||<^> ||<^>Mirror image reverse brain before morphing||
||<^>Algorithm||<^>-rotate||<^> <dalpha, dbeta, dgamma (floats)> ||<^>Rotates brain by dalpha, dbeta, dgamma||
||<^>Algorithm||<^>-S||<^> <scale (float)> ||<^>Scales distances by {scale}||
||<^>Algorithm||<^>-search||<^> ||<^>Integrating with binary search line minimization||
||<^>Algorithm||<^>-spring||<^> <l_spring (float)> ||<^>||
||<^>Algorithm||<^>-tol||<^> <tol (float)> ||<^>Tolerance?||
||<^>Algorithm||<^>-topology||<^> ||<^>Preserves the topology of positive area triangles||
||<^>Algorithm||<^>-vnum, -distances||<^> <nbhd_size, max_nbrs (floats)> ||<^>Sets neighborhood parameters||
||<^>Algorithm||<^>-vsmooth||<^> ||<^>Use space/time varying smoothness weighting||
||<^>Algorithm||<^>-W||<^> <write_iterations (int)> ||<^>Also triggers diagnostics||
||<^>Utility||<^>-?, -H, -U||<^> ||<^>print_help()||
||<^>Utility||<^>--help||<^> ||<^>print_help||
||<^>Utility||<^>-V||<^> <Gdiag_no (int)> ||<^>Supplies a vertex number for diagnostics||
||<^>Utility||<^>-vector||<^> ||<^>Prints some help for Multiframe mode including listing field names/numbers||
||<^>Utility||<^>--version||<^> ||<^>print_version()||
||<^>Footer||<^>XXXXXXXXXXXXX||<^> ||<^>||
 
= Outputs =
|| volume1 || description ||
|| volume2 || description ||

= Description =
 This program register a surface with  an average surface.

= Examples =
== Example 1 ==
Command:
Description:

== Example 2 ==
Command:
Description:

= Bugs =
None

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

= Links =
FreeSurfer, FsFast

= Methods Description =
{{{
N/a
}}}

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

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

= Document Authors =
DougGreve, BruceFischl, GrahamWideman