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Software version described: * $Date: 2007/12/28 00:49:46 $ * $Revision: 1.50 $ * Use usage or version option to see version you are using |
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mris_register - This program register a surface with an average surface | mris_register - This program registers a surface to an average surface template |
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|| input surface || || || || average surface || || || || output surface || || || |
||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''|| ||<^>1||<^> <surf_fname> ||<^>Input surface to register, often {hemi}.sphere|| ||<^>2||<^> <template_fname> ||<^>Template file for average surface. (See also flagged args that can modify this)|| ||<^>3||<^> <out_fname> ||<^>Output surface file to capture registration. Example: {hemi}.sphere.reg|| |
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|| -overlay <overlay name> <smoothing level> || arbitrary scalar field over the surface to drive the registration || || || -flag4 ?? || brief description || || |
||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''|| ||<^>Input||<^>-1||<^> ||<^>(One) Treats target as a single subject's surface not a template file|| ||<^>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||<^> ||<^>|| |
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= Author/s = DougGreve, BruceFischl |
= Document Authors = DougGreve, BruceFischl, GrahamWideman |
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
Synopsis
mris_register [options] <input surface> <average surface> <output surface>
Arguments
Positional Arguments
Posn |
<Argname> |
Description |
1 |
<surf_fname> |
Input surface to register, often {hemi}.sphere |
2 |
<template_fname> |
Template file for average surface. (See also flagged args that can modify this) |
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 as a single subject's surface not a template file |
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
Methods Description
N/a
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>