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Software version described:
 * $Date: 2006/12/29 02:09:07 $
 * $Revision: 1.25 $
 * Use usage or version option to see version you are using

= Name =
mri_make_template 

= Overview =
Reads data from two or more subjects and creates a template file for volumes. (as opposed to [[mris_make_template]] which makes a template for registering surfaces.)

= Synopsis =
mri_make_template [Flagged args] subject1 [subject2...] ouput_template_path

= Arguments =
== Positional Arguments ==
||<^>'''Posn'''||<^> <'''Argname'''> ||<^>'''Description'''||
||<^>1 to last-1||<^> <subject> ||<^>List of one or more subjects to input||
||<^>last||<^> <Out_fname> ||<^>Full path to output template file.||

== Required Flagged Arguments ==
None

== Optional Flagged Arguments ==
||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''||
||<^>Input||<^>-open||<^> <open> ||<^>Open input volume {open} times||
||<^>Input||<^>-sdir||<^> <subjects_dir> ||<^>Sets SUBJECTS_DIR instead of default||
||<^>Input||<^>-T1||<^> <T1_name> ||<^>Reads T1 volume from directory T1_name. (Or file, presumably?)||
||<^>Output||<^>-B||<^> <binary_name> ||<^>Generates binary template from {binary_name} volume||
||<^>Output||<^>-novar||<^> ||<^>Disables writing of variance estimates||
||<^>Output||<^>-S,-V||<^> <var_fname> ||<^>Writes variances||
||<^>Output||<^>-statsonly||<^> ||<^>||
||<^>Output||<^>-X||<^> <xform_mean_fname, xform_covariance_fname> ||<^>Writes means and covariances of xforms||
||<^>Algorithm||<^>-binarize||<^> <binarize (int)> ||<^>Binarizes input volume with thresh= binarize||
||<^>Algorithm||<^>-erode||<^> <erode> ||<^>Erodes input volume {erode} times||
||<^>Algorithm||<^>-N||<^> ||<^>Don't use transform on first volume||
||<^>Algorithm||<^>-smooth||<^> <smooth (float)> ||<^>Smooths output with Gaussian sigma= smooth||
||<^>Algorithm||<^>-T||<^> <transform_fname> ||<^>Applies transformation {transform_fname} to each volume||
||<^>Utility||<^>-?,-U||<^> ||<^>Print usage||
||<^>Footer||<^>XXXXXXXXXXXXX||<^> ||<^>||

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

= Description =
Not sure what kind of template this produces, nor what registration is expected upstream from the is program. --GW

= Examples =
== Example 1 ==
??

description

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

description

= Bugs =
None

= See Also =
[[mris_make_template]]

= Links =
FreeSurfer, FsFast

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

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

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

= Documentation Authors =
BruceFischl, GrahamWideman