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>