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= Purpose =
Xxx
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mri_make_template subject1 subject2 ... output mri_make_template subject1 [subject2 ...] output
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None ||<^>'''Category'''||<^>'''Flag'''||<^> <'''Args'''> ||<^>'''Description'''||
||<^>Input||<^> -sulc||<^> <othercurv> ||<^>Sets curvature_names[1] = othercurv. Default is 'curv'.||
||<^>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||
||<^>Atlas config||<^>-addframe||<^> <which_field where_in_atlas> ||<^>Uses the two integer args to specify how to add a variable to the atlas.[[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.||
||<^>Atlas 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]);||
||<^>Atlas config||<^>-overlay||<^> <overlay_file> ||<^>Increases atlas_size by one (to makes space for additional atlas variable) and reads overlay file from {subject}/label/{overlay_file}. To change directory, use -overlay_dir option||
||<^>Atlas config||<^>-size||<^> <atlas_size> ||<^>Sets the atlas 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>Docs for this are 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.||
||<^>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: an atlas 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||<^> ||<^>||

Navigation(children) Index TableOfContents

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

mri_make_template

Purpose

Xxx

Synopsis

mri_make_template subject1 [subject2 ...] output

Arguments

Positional Arguments

subject1

description

subject2

description

output

description

Required Flagged Arguments

None

Optional Flagged Arguments

Category

Flag

<Args>

Description

Input

-sulc

<othercurv>

Sets curvature_names[1] = othercurv. Default is 'curv'.

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

Atlas config

-addframe

<which_field where_in_atlas>

Uses the two integer args to specify how to add a variable to the atlas.BR BRwhich_field specifies the variable to add, with the meaning of the number determined by the list you can get from the vector option.BRBRwhere_in_atlas tells what order to place the new field/ Locations 0..2 are already occupied by the default variables.

Atlas config

-nodefault

Not sure the purpose of this option --GWBRBRbase_default=0;BRBRatlas_size = 0;BRBRparms->nfields=0;BRBRfor (n=0;n<3;n++)BRBRInitFieldLabel(&parms->fields[n]);

Atlas config

-overlay

<overlay_file>

Increases atlas_size by one (to makes space for additional atlas variable) and reads overlay file from {subject}/label/{overlay_file}. To change directory, use -overlay_dir option

Atlas config

-size

<atlas_size>

Sets the atlas 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>Docs for this are wrong (--GW):BRBRUsage: -norot : 'align before averaging'BRBR-norot printout: 'not aligning hemispheres before averaging'BRBRWhat source code appears to do:BRBRIf -norot is selected, program appears to skip performing rigid alignment of subject's surface to template before averaging.BRBRThis 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.

Algorithm

-rot

-rot printout: 'rigidly aligning hemispheres before averaging.' BRie: DO perform rigid alignment of subject's surface to template before averaging.BRBRWhat source code appears to do:BRBRFor multiframes situation: always perform rigid alignment.BRBRFor 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: an atlas 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"]

Links

FreeSurfer, FsFast

Methods Description

??

References

["References/Lastname###"]

Reporting Bugs

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

Documentation Authors

BruceFischl, GrahamWideman

mri_make_template (last edited 2008-04-29 11:45:52 by localhost)