NAME

mris_register

SYNOPSIS

mris_register [options] <surf_fname> <target> <out_fname>

DESCRIPTION

This program registers a surface to an average surface template.

POSITIONAL ARGUMENTS

ArgumentExplanation
<surf_fname>Input: Surface to register, often {hemi}.sphere
<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.
<out_fname>Output surface file to capture registration. Example: {hemi}.sphere.reg

REQUIRED-FLAGGED ARGUMENTS

*******************************************************************

OPTIONAL-FLAGGED ARGUMENTS

ArgumentExplanation
-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?)
-addframe <which_field, where_in_atlas (ints)>Add field which_field with location where_in_atlas in the atlas
-annot <annot_name>Zeroes medial wall using annotation {annot_name}
-C <curvature_fname> 
-canon <canon_name>Use surface {canon_name} for canonical properties
-inflatedUse inflated surface for initial alignment
-infname <name>Uses {name} for inflated surface, for initial alignment. Sets inflated_name, surface_name and curvature_names[0]
-L <labelfile atlas_gcsa_file label_name>Specify a manual label to align with atlas label <label name>
-O <orig_name>Use {orig_name} for original properties
-overlay <overlay_file navgs(int)>Adds a variable to the atlas from {overlay_file}, smoothing it {navgs} times. {subject}/labels/{hemi}.{overlay_file}
-overlay-dir <overlay_dir>Changes overlay path: {subject}/{overlay_dir}/{hemi}.{overlay_file}
-sreg <starting_reg_fname>Start registration with coordinates in file starting_reg_fname
-jacobian <jacobian_fname>Write out jacobian of mapping to file jacobian_fname
-A <n_averages (int)> 
-adaptiveUse adaptive time step integration
-area <l_area (float)>Sets l_area
-corr <l_corr (float)> 
-curvUse smoothwm curvature for final alignment
-dist <l_dist (float)>Specify distance term. Sets l_dist and also use_defaults = 0
-dt <dt (float)>Sets momentum with dt
-dt_dec <dt_decrease (float)> 
-dt_inc <dt_increase (float)> 
-E <l_external (float)> 
-error_ratio <error_ratio (float)> 
-initUse initial registration
-lap <lap (float)>l_laplacian
-lmIntegrate using line minimization
-M <momentum (float)>Chooses integration_type = INTEGRATE_MOMENTUM and sets momentum value
-max_degrees <max_degrees (float)>Set max angle for search to max_degrees
-medianUses median normalization (instead of mean).
-min_degrees <min_degrees (float)>Set min angle for search to min_degrees
-multi_scale <multi_scale (int)>Use multi_scale scales for morphing
-N <niterations (int)> 
-nangles <nangles (int)>Set # of angles/search per scale to nangles
-nbrs <nbrs (int)>Use neighborhood size=nbrs
-nlarea <l_nlarea (float)>Sets l_nlarea
-nocurvDo not use smoothwm curvature for final alignment
-nonormDisables normalization
-norotDisables initial rigid alignment
-nosulcDisables initial sulc alignment
-nsurfaces <nsurfaces>Use nsurfaces surfaces/curvatures for alignment
-ocorr <l_ocorr (float)>Sets overlay correlation coefficient to l_ocorr
-P <max_passes (int)>Limit unfolding to {max_passes} passes
-parea <l_parea (float)>Sets l_parea
-remove_negative <remove_negative (int)>Non-zero to remove negative triangles with iterative smoothing, or 0 to skip that
-reverseMirror image reverse brain before morphing
-rotate <dalpha, dbeta, dgamma (floats)>Rotates brain by dalpha, dbeta, dgamma
-S <scale (float)>Scales distances by {scale}
-searchIntegrating with binary search line minimization
-spring <l_spring (float)> 
-tol <tol (float)>Tolerance?
-topologyPreserves the topology of positive area triangles
-vnum, -distances <nbhd_size, max_nbrs (floats)>Sets neighborhood parameters
-vsmoothUse space/time varying smoothness weighting
-W <write_iterations (int)>Also triggers diagnostics
-?, -H, -U, --helpprint help
-V <Gdiag_no (int)>Supplies a vertex number for diagnostics
-vectorPrints some help for Multiframe mode including listing field names/numbers
--versionprint version

REPORTING

Report bugs to <freesurfer@nmr.mgh.harvard.edu>