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Software version described:
 * $Date: 2007/02/13 12:20:16 $
 * $Revision: 1.23 $
 * Use usage or version option to see version you are using

= Name =
mris_make_template 

= Overview =
This program reads surface and curvature data from multiple subjects and produces a "template". This template is later used by [[mris_register]] to register the sphere surface of individual subjects to the average surface.

Related concepts are discussed here: SurfaceRegAndTemplates.

"Atlas" vs "Template": Descriptions below sometimes refer to "atlas", following the usage in this program's source code and some of its messages. However, the file produced by this program is normally referred to as a "template" file, as distinct from "atlas" which is generally used for the GCA files that capture reference maps of regions. (See also [[mris_ca_train]].) 

= Synopsis =
mri_make_template [Flagged args] hemi sphere_name subject1 [subject2 ...] template_name

= Arguments =
== Positional Arguments ==

||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''||
||<^>1||<^> <hemi> ||<^>lh or rh||
||<^>2||<^> <sphere_name> ||<^>Name of sphere surface to read from each subject. Actual filepath will be:<<BR>><<BR>>{subject}/surf/{sphere_name}.{hemi}||
||<^>3 to last-1||<^> <subject> ||<^>List of one or more subjects whose sphere files will be input.||
||<^>last||<^> <template_path> ||<^>Full path to template file. If tempate already exists, it will be input, used to register subjects and new variables will be added to it. If it does not exist it will be created, and initial data created from the first subject.||

== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
Note: single-letter flags can be upper or lower case.<<BR>>
MMTable
||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''||
||<^>Input||<^> -sulc||<^> <othercurv> ||<^>Sets curvature_names[1] (of 0..2) to othercurv. Default is 'sulc'.||
||<^>Input||<^>-infname||<^> <surffilename> ||<^#FFFF80>Sets surface_names[0] = surffilename, and curvature_names[0] = surffilename'.H'. Default is 'inflated'. (Not sure what a '.H' file is or where it comes from. --GW).||
||<^>Input||<^>-O||<^> <surface_name> ||<^>Sets a different surface_name for surface_names 1 and 2 (of 0,1,2), instead of default smoothwm.||
||<^>Input||<^>-overlay-dir||<^> <overlay_dir> ||<^>Sets directory from which to read optional overlay file. Default 'label'.||
||<^>Input||<^>-sdir||<^> <subjects_dir> ||<^>Set SUBJECTS_DIR to subjects_dir||
||<^>Template config||<^>-addframe||<^> <which_field   where_in_atlas> ||<^>Uses the two integer args to specify how to add a variable to the atlas (ie: template).<<BR>> <<BR>>which_field specifies the variable to add, with the meaning of the number determined by the list you can get from the vector option.<<BR>><<BR>>where_in_atlas tells what order to place the new field/ Locations 0..2 are already occupied by the default variables.||
||<^>Template config||<^>-nodefault||<^> ||<^>Not sure the purpose of this option --GW<<BR>><<BR>>base_default=0;<<BR>><<BR>>atlas_size = 0;<<BR>><<BR>>parms->nfields=0;<<BR>><<BR>>for (n=0;n<3;n++)<<BR>><<BR>>InitFieldLabel(&parms->fields[n]);||
||<^>Template config||<^>-overlay||<^> <overlay_file> ||<^>Increases atlas_size by one (to makes space for additional template variable) and reads overlay file from {subject}/label/{overlay_file}.  To change directory, use -overlay_dir option||
||<^>Template config||<^>-size||<^> <atlas_size> ||<^>Sets the atlas (ie: template) to be able to contain data for atlas_size number of variables for each vertex. Default is atlas_size=3.||
||<^>Algorithm||<^>-A||<^> <navgs> ||<^>Average curvature patterns navgs times||
||<^>Algorithm||<^>-annot||<^> <annot_name> ||<^>Zero the median wall. Ie: Causes program to read annotation file from which to find vertices that belong to the medial wall so that these can be given a curvature of zero. Rationale?||
||<^>Algorithm||<^>-median||<^> ||<^>Using median normalization (default is mean)||
||<^>Algorithm||<^>-nbrs||<^> <nbrs> ||<^>Set neighborhood size to nbrs||
||<^>Algorithm||<^>-norot||<^> ||<^#FFFF80>Help/usage info for this is wrong (--GW):<<BR>><<BR>>Usage: -norot : 'align before averaging'<<BR>><<BR>>-norot printout: 'not aligning hemispheres before averaging'<<BR>><<BR>>What source code appears to do:<<BR>><<BR>>If -norot is selected, program appears to skip performing rigid alignment of subject's surface to template before averaging.<<BR>><<BR>>This appears to be the default, which is surprising because in addition to the Usage info describing this option wrongly, Usage does not mention the '-rot' option.<<BR>> Fixed in version 1.23.2.1||
||<^>Algorithm||<^>-rot||<^> ||<^>-rot printout: 'rigidly aligning hemispheres before averaging.' <<BR>>ie: DO perform rigid alignment of subject's surface to template before averaging.<<BR>><<BR>>What source code appears to do:<<BR>><<BR>>For multiframes situation: always perform rigid alignment.<<BR>><<BR>>For NOT multiframe situation: perform rigid alignment for all subjects except for the first. (Presumably the first subject is used to create the initial template data?)||
||<^>Algorithm||<^>-S||<^> <scale> ||<^>Scale 'parameterization' by scale (float).  (If 'parameterization' refers to a complete surface worth of per-vertex values (ie: a template variable), is the idea here to scale '''all''' those variables by the same amount? --GW)||
||<^>Utility||<^>-?, -U||<^> ||<^>print_usage()||
||<^>Utility||<^>-help, --help||<^> ||<^>print_help()||
||<^>Utility||<^>-vector||<^> ||<^>Prints some help for using Multiframe mode. Option presumably named 'vector' because multiframe mode means that the template has multiple values per vertex.||
||<^>Utility||<^>-version, --version||<^> ||<^>print_version()||
||<^>Utility||<^>-W||<^> <optional int> ||<^>Obsolete option. Ignored.||
||<^>Footer||<^>XXXXXXXXXXXXX||<^> ||<^>||

= Outputs =
|| output || ?? ||

= Description =
??

= Examples =
== Example 1 ==
??

description

== Example 2 ==
command foo -i f -o out -f fvalue

description

= Bugs =
None

= See Also =
[[mris_make_template]], SurfaceRegAndTemplates

= Links =
FreeSurfer, FsFast

= Methods Description =
{{{
??
}}}

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

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

= Documentation Authors =
DougGreve, BruceFischl, GrahamWideman