mris_register
mris_register [options] <surf_fname> <target> <out_fname>
This program registers a surface to an average surface template.
Argument | Explanation |
---|---|
<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 |
Argument | Explanation |
---|---|
-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 |
-inflated | Use 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)> | |
-adaptive | Use adaptive time step integration |
-area <l_area (float)> | Sets l_area |
-corr <l_corr (float)> | |
-curv | Use 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)> | |
-init | Use initial registration |
-lap <lap (float)> | l_laplacian |
-lm | Integrate 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 |
-median | Uses 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 |
-nocurv | Do not use smoothwm curvature for final alignment |
-nonorm | Disables normalization |
-norot | Disables initial rigid alignment |
-nosulc | Disables 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 |
-reverse | Mirror image reverse brain before morphing |
-rotate <dalpha, dbeta, dgamma (floats)> | Rotates brain by dalpha, dbeta, dgamma |
-S <scale (float)> | Scales distances by {scale} |
-search | Integrating with binary search line minimization |
-spring <l_spring (float)> | |
-tol <tol (float)> | Tolerance? |
-topology | Preserves the topology of positive area triangles |
-vnum, -distances <nbhd_size, max_nbrs (floats)> | Sets neighborhood parameters |
-vsmooth | Use space/time varying smoothness weighting |
-W <write_iterations (int)> | Also triggers diagnostics |
-?, -H, -U, --help | print help |
-V <Gdiag_no (int)> | Supplies a vertex number for diagnostics |
-vector | Prints some help for Multiframe mode including listing field names/numbers |
--version | print version |
Report bugs to <freesurfer@nmr.mgh.harvard.edu>